Resource List
List all resources, or create a new resource.
GET /api/t/?function=%22Sequence+analysis%22
{ "count": 1137, "next": "?page=2", "previous": null, "list": [ { "name": "trackViewer", "description": "Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.", "homepage": "https://bioconductor.org/packages/trackViewer", "biotoolsID": "trackviewer", "biotoolsCURIE": "biotools:trackviewer", "version": [ "1.48.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_3184", "term": "Sequence assembly visualisation" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "R" ], "license": "GPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/trackViewer_1.48.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/trackViewer", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/s41592-019-0430-y", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Jianhong Ou", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Julie Lihua Zhu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:06:16Z", "lastUpdate": "2026-10-02T16:04:49.533911Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IsoformSwitchAnalyzeR", "description": "Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.", "homepage": "https://bioconductor.org/packages/IsoformSwitchAnalyzeR", "biotoolsID": "isoformswitchanalyzer", "biotoolsCURIE": "biotools:isoformswitchanalyzer", "version": [ "2.12.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2451", "term": "Sequence comparison" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": "The basic input is a replicate transcript/isoform expression matrix as well as the genomic coordinates of the transcript/isoforms. The output is a list of (prioritized) isoform switches with predicted consequences.", "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "R" ], "license": "GPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioconductor.org/packages/IsoformSwitchAnalyzeR/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://bioconductor.org/packages/IsoformSwitchAnalyzeR/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/IsoformSwitchAnalyzeR", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btz247", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1158/1541-7786.MCR-16-0459", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Chunxu Han", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Elena Iriondo Delgado", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jeroen Gilis", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Kristoffer Vitting-Seerup", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "KVS", "additionDate": "2017-06-13T08:49:49Z", "lastUpdate": "2026-10-02T15:59:43.846795Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HIBAG", "description": "It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. It can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging (improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection), an ensemble classifier method, with haplotype inference for SNPs and HLA types.", "homepage": "https://bioconductor.org/packages/HIBAG", "biotoolsID": "hibag", "biotoolsCURIE": "biotools:hibag", "version": [ "1.48.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_0804", "term": "Immunology" }, { "uri": "http://edamontology.org/topic_2830", "term": "Immunoproteins and antigens" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://github.com/zhengxwen/HIBAG", "type": [ "Mirror" ], "note": null }, { "url": "http://www.biostat.washington.edu/~bsweir/HIBAG/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/zhengxwen/HIBAG", "type": "Source code", "note": null, "version": null }, { "url": "https://hibag.s3.amazonaws.com/index.html", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/HIBAG", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-8546-3_11", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Bruce Weir", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Xiuwen Zheng", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:03:50Z", "lastUpdate": "2026-10-02T15:59:09.727543Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GenomicAlignments", "description": "Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.", "homepage": "https://bioconductor.org/packages/GenomicFeatures", "biotoolsID": "genomicalignments", "biotoolsCURIE": "biotools:genomicalignments", "version": [ "1.64.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3563", "term": "RNA-seq read count analysis" }, { "uri": "http://edamontology.org/operation_3230", "term": "Read depth analysis" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2306", "term": "GTF" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2306", "term": "GTF" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/GenomicFeatures", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/GenomicFeatures", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1003118", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "D. Sarkar", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "D. Tenenbaum", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "D. Van Twisk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "H. Pagès", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "J. MacDonald", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "L. Shepherd", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "M. Carlson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "M. Lawrence", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "M. Morgan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "M. Ramos", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "P. Aboyoun", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "P. Shannon", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "S. Arora", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "S. Falcon", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "S. Saini", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "V. Obenchain", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:32Z", "lastUpdate": "2026-10-02T15:58:36.202078Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "esATAC", "description": "This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.", "homepage": "https://bioconductor.org/packages/esATAC", "biotoolsID": "esatac", "biotoolsCURIE": "biotools:esatac", "version": [ "1.34.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" }, { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "C++", "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/wzthu/esATAC", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/esATAC", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty141", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Wei Zhang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Zheng Wei", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-07-01T12:52:10Z", "lastUpdate": "2026-10-02T15:57:50.866333Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BiocParallel", "description": "This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.", "homepage": "https://bioconductor.org/packages/BiocParallel", "biotoolsID": "biocparallel", "biotoolsCURIE": "biotools:biocparallel", "version": [ "1.46.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/BioConductor/BiocParallel", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/Bioconductor/BiocParallel", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/BiocParallel", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.BiocParallel", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Aaron Lun", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Henrik Bengtsson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiefei Wang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Madelyn Carlson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Martin Morgan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Michel Lang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Nitesh Turaga", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Phylis Atieno", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ryan Thompson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Sergio Oller", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Valerie Obenchain", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:04:28Z", "lastUpdate": "2026-10-02T15:55:50.620930Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "R453Plus1Toolbox", "description": "The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.", "homepage": "https://bioconductor.org/packages/R453Plus1Toolbox", "biotoolsID": "r453plus1toolbox", "biotoolsCURIE": "biotools:r453plus1toolbox", "version": [ "1.62.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "LGPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/R453Plus1Toolbox_1.62.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/R453Plus1Toolbox", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Christian Ruckert", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Christoph Bartenhagen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Hans-Ulrich Klein", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:37Z", "lastUpdate": "2026-09-30T22:22:04.088557Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "QDNAseq", "description": "Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.", "homepage": "https://bioconductor.org/packages/QDNAseq", "biotoolsID": "qdnaseq", "biotoolsCURIE": "biotools:qdnaseq", "version": [ "1.48.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-1.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ccagc/QDNAseq", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/ccagc/QDNAseq", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/QDNAseq", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Daoud Sie", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Erik van Dijk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Henrik Bengtsson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ilari Scheinin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:04Z", "lastUpdate": "2026-09-30T22:21:52.061857Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PharmacoGx", "description": "Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.", "homepage": "https://bioconductor.org/packages/PharmacoGx", "biotoolsID": "pharmacogx", "biotoolsCURIE": "biotools:pharmacogx", "version": [ "3.16.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0208", "term": "Pharmacogenomics" }, { "uri": "http://edamontology.org/topic_0202", "term": "Pharmacology" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-3.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/PharmacoGx_3.16.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/PharmacoGx", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Benjamin Haibe-Kains", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Christopher Eeles", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Feifei Li", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jermiah Joseph", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Mark Freeman", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Petr Smirnov", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Zhaleh Safikhani", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:56:33Z", "lastUpdate": "2026-09-30T22:21:28.230032Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "InteractionSet", "description": "Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.", "homepage": "https://bioconductor.org/packages/InteractionSet", "biotoolsID": "interactionset", "biotoolsCURIE": "biotools:interactionset", "version": [ "1.40.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/InteractionSet_1.40.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/InteractionSet", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Aaron Lun", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Elizabeth Ing-Simmons", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Malcolm Perry", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:56:07Z", "lastUpdate": "2026-09-30T22:18:53.676886Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HTqPCR", "description": "Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).", "homepage": "https://bioconductor.org/packages/HTqPCR", "biotoolsID": "htqpcr", "biotoolsCURIE": "biotools:htqpcr", "version": [ "1.66.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3519", "term": "PCR experiment" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.ebi.ac.uk/bertone/software", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://www.ebi.ac.uk/bertone/software", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/HTqPCR", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Heidi Dvinge", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Paul Bertone", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:27Z", "lastUpdate": "2026-09-30T22:18:32.578612Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Guitar", "description": "The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.", "homepage": "https://bioconductor.org/packages/Guitar", "biotoolsID": "guitar", "biotoolsCURIE": "biotools:guitar", "version": [ "2.28.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3586", "term": "bed12" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/Guitar_2.28.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/Guitar", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Hui Liu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jia Meng", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Lin Zhang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Xiao Du", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:34Z", "lastUpdate": "2026-09-30T22:18:13.523112Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "groHMM", "description": "A pipeline for the analysis of GRO-seq data.", "homepage": "https://bioconductor.org/packages/groHMM", "biotoolsID": "grohmm", "biotoolsCURIE": "biotools:grohmm", "version": [ "1.46.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0415", "term": "Nucleic acid feature detection" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3006", "term": "bigWig" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3547", "term": "Image format" }, { "uri": "http://edamontology.org/format_3005", "term": "WIG" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3006", "term": "bigWig" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3547", "term": "Image format" }, { "uri": "http://edamontology.org/format_3005", "term": "WIG" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3006", "term": "bigWig" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3547", "term": "Image format" }, { "uri": "http://edamontology.org/format_3005", "term": "WIG" } ] }, { "data": { "uri": "http://edamontology.org/data_1017", "term": "Sequence range" }, "format": [ { "uri": "http://edamontology.org/format_3006", "term": "bigWig" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3547", "term": "Image format" }, { "uri": "http://edamontology.org/format_3005", "term": "WIG" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Kraus-Lab/groHMM", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/Kraus-Lab/groHMM", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/groHMM", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Andre Martins", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Anusha Nagari", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Charles G. Danko", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Minho Chae", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pariksheet Nanda", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Tulip Nandu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Maintainer" ], "note": null }, { "name": "W. Lee Kraus", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:55:57Z", "lastUpdate": "2026-09-30T22:18:04.587374Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DECIPHER", "description": "A toolset for deciphering and managing biological sequences.", "homepage": "https://bioconductor.org/packages/DECIPHER", "biotoolsID": "decipher", "biotoolsCURIE": "biotools:decipher", "version": [ "3.8.1" ], "otherID": [], "relation": [ { "biotoolsID": "s4vectors", "type": "uses" }, { "biotoolsID": "xvector", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Proteomics", "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://DECIPHER.codes", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/DECIPHER", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Erik Wright", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:30Z", "lastUpdate": "2026-09-30T22:15:56.983231Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cummeRbund", "description": "Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.", "homepage": "https://bioconductor.org/packages/cummeRbund", "biotoolsID": "cummerbund", "biotoolsCURIE": "biotools:cummerbund", "version": [ "2.54.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/cummeRbund_2.16.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/cummeRbund", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "C. Trapnell", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "D. Kelley", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "L. Goff", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:00:36Z", "lastUpdate": "2026-09-30T22:15:43.985474Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CSAR", "description": "Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.", "homepage": "https://bioconductor.org/packages/CSAR", "biotoolsID": "csar", "biotoolsCURIE": "biotools:csar", "version": [ "1.64.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/CSAR_1.64.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/CSAR", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Jose M Muino", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:59:54Z", "lastUpdate": "2026-09-30T22:15:37.267693Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "compEpiTools", "description": "Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.", "homepage": "https://bioconductor.org/packages/compEpiTools", "biotoolsID": "compepitools", "biotoolsCURIE": "biotools:compepitools", "version": [ "1.46.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3744", "term": "Multiple sample visualisation" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3173", "term": "Epigenomics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-1.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/compEpiTools_1.46.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/compEpiTools", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-015-0742-6", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Kamal Kishore", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Mattia Furlan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Maintainer" ], "note": null }, { "name": "Mattia Pelizzola", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:08Z", "lastUpdate": "2026-09-30T22:15:12.320253Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ChIPQC", "description": "Quality metrics for ChIPseq data.", "homepage": "https://bioconductor.org/packages/ChIPQC", "biotoolsID": "chipqc", "biotoolsCURIE": "biotools:chipqc", "version": [ "1.48.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-3.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/ChIPQC_1.48.3.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/ChIPQC", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Ines de Santiago", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Rory Stark", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Tom Carroll", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Wei Liu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:59:52Z", "lastUpdate": "2026-09-30T22:14:41.036599Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Chicago", "description": "A pipeline for analysing Capture Hi-C data.", "homepage": "https://bioconductor.org/packages/Chicago", "biotoolsID": "chicago", "biotoolsCURIE": "biotools:chicago", "version": [ "1.40.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/Chicago_1.40.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/Chicago", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Jonathan Cairns", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Mikhail Spivakov", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Paula Freire Pritchett", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Steven Wingett", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:55:15Z", "lastUpdate": "2026-09-30T22:14:35.826488Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bumphunter", "description": "Tools for finding bumps in genomic data", "homepage": "https://bioconductor.org/packages/bumphunter", "biotoolsID": "bumphunter", "biotoolsCURIE": "biotools:bumphunter", "version": [ "1.54.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ririzarr/bumphunter", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/rafalab/bumphunter", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/bumphunter", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btu049", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/ije/dyr238", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Andrew E. Jaffe", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Harris Jaffee", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Hector Corrada Bravo", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kasper Daniel Hansen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Leonardo Collado-Torres", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Martin Aryee", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Rafael A. Irizarry", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Shan Andrews", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Tamilselvi Guharaj", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:02:52Z", "lastUpdate": "2026-09-30T22:14:16.076347Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BaalChIP", "description": "The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.", "homepage": "https://bioconductor.org/packages/BaalChIP", "biotoolsID": "baalchip", "biotoolsCURIE": "biotools:baalchip", "version": [ "1.38.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/BaalChIP_1.38.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/BaalChIP", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Bruce Ponder", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Chandra SR Chilamakuri", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Florian Markowetz", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Ines de Santiago", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Ke Yuan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Kerstin Meyer", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Martin O'Reilly", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Wei Liu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:55:04Z", "lastUpdate": "2026-09-30T22:12:45.708235Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fastseg", "description": "fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments.", "homepage": "https://bioconductor.org/packages/fastseg", "biotoolsID": "fastseg", "biotoolsCURIE": "biotools:fastseg", "version": [ "1.58.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "LGPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.bioinf.jku.at/software/fastseg/fastseg.html", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://www.bioinf.jku.at/software/fastseg/index.html", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/fastseg", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks003", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Alexander Blume", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Guenter Klambauer", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Sonali Kumari", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:00:14Z", "lastUpdate": "2026-09-29T12:42:53.847984Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "tripr", "description": "TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.", "homepage": "https://bioconductor.org/packages/tripr", "biotoolsID": "TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler", "biotoolsCURIE": "biotools:TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler", "version": [ "1.18.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2830", "term": "Immunoproteins and antigens" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "MIT", "collectionID": [ "BioConductor" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Greece" ], "elixirCommunity": [], "link": [ { "url": "https://www.bioconductor.org/packages/devel/bioc/html/tripr.html", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/BiodataAnalysisGroup/tripr", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/tripr", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-020-03669-1", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Anastasia Chatzidimitriou", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Andreas Agathangelidis", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Aspasia Orfanou", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Chrysi Galigalidou", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Elisavet Vlachonikola", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Fotis E. Psomopoulos", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Iason Ofeidis", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Katerina Gemenetzi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kostas Stamatopoulos", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Maria Th. Kotouza", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Nikolaos Pechlivanis", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Pericles A. Mitkas", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Raphael Sandaltzopoulos", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "fpsom", "additionDate": "2020-02-21T13:12:50Z", "lastUpdate": "2026-09-06T02:02:11.073957Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Biostrings", "description": "Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.", "homepage": "https://bioconductor.org/packages/Biostrings", "biotoolsID": "biostrings", "biotoolsCURIE": "biotools:biostrings", "version": [ "2.80.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Loading" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3115", "term": "Microarray metadata" }, "format": [ { "uri": "http://edamontology.org/format_2061", "term": "Nucleic acid features (primers) format" }, { "uri": "http://edamontology.org/format_1919", "term": "Sequence record format" }, { "uri": "http://edamontology.org/format_2554", "term": "Alignment format (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2061", "term": "Nucleic acid features (primers) format" }, { "uri": "http://edamontology.org/format_1919", "term": "Sequence record format" }, { "uri": "http://edamontology.org/format_2554", "term": "Alignment format (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2061", "term": "Nucleic acid features (primers) format" }, { "uri": "http://edamontology.org/format_1919", "term": "Sequence record format" }, { "uri": "http://edamontology.org/format_2554", "term": "Alignment format (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3115", "term": "Microarray metadata" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/Biostrings", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/Biostrings", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.Biostrings", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Aidan Lakshman", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Albert Vill", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Beryl Kanali", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Erik Wright", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Felix Ernst", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Haleema Khan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Hervé Pagès", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Jen Wokaty", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Kieran O'Neill", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Marcel Ramos", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Nicolas Delhomme", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Patrick Aboyoun", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Robert Gentleman", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Saikat DebRoy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Valerie Obenchain", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Vince Carey", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wolfgang Huber", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:29Z", "lastUpdate": "2026-09-06T01:51:43.641526Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "tracktables", "description": "Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.", "homepage": "https://bioconductor.org/packages/tracktables", "biotoolsID": "tracktables", "biotoolsCURIE": "biotools:tracktables", "version": [ "1.46.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3744", "term": "Multiple sample visualisation" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3763", "term": "Service invocation" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-3.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/tracktables_1.46.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/tracktables", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.tracktables", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Anne Pajon", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Sanjay Khadayate", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Tom Carroll", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Ziwei Liang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:05:57Z", "lastUpdate": "2026-09-01T07:12:00.530208Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SICtools", "description": "This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.", "homepage": "https://bioconductor.org/packages/SICtools", "biotoolsID": "sictools", "biotoolsCURIE": "biotools:sictools", "version": [ "1.42.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/SICtools_1.42.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/SICtools", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.SICtools", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Wu Wei", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Xiaobin Xing", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:03Z", "lastUpdate": "2026-09-01T07:08:43.943790Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Rsubread", "description": "Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.", "homepage": "https://bioconductor.org/packages/Rsubread", "biotoolsID": "rsubread", "biotoolsCURIE": "biotools:rsubread", "version": [ "2.26.0" ], "otherID": [ { "value": "RRID:SCR_016945", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioconductor.org/packages/release/bioc/html/Rsubread.html", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://bioconductor.org/packages/Rsubread", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/Rsubread", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkz114", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Wei Shi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Yang Liao and Gordon K Smyth with contributions from Jenny Dai", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:56:55Z", "lastUpdate": "2026-09-01T07:06:09.410952Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Rhtslib", "description": "This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package=\"Rhtslib\", \"Rhtslib\").", "homepage": "https://bioconductor.org/packages/Rhtslib", "biotoolsID": "rhtslib", "biotoolsCURIE": "biotools:rhtslib", "version": [ "3.8.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "LGPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.htslib.org/", "type": [ "Mirror" ], "note": null }, { "url": "https://github.com/nhayden/Rhtslib", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/", "type": "Source code", "note": null, "version": null }, { "url": "https://bioconductor.org/packages/Rhtslib", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/Rhtslib", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.Rhtslib", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Hervé Pagès", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Jeroen Ooms", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Martin Morgan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Nathaniel Hayden", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Tomas Kalibera", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:38Z", "lastUpdate": "2026-09-01T07:05:07.296034Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "r3Cseq", "description": "This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.", "homepage": "https://bioconductor.org/packages/r3Cseq", "biotoolsID": "r3cseq", "biotoolsCURIE": "biotools:r3cseq", "version": [ "1.58.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://r3cseq.genereg.net", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://r3cseq.genereg.net", "type": "Source code", "note": null, "version": null }, { "url": "https://github.com/supatt-lab/r3Cseq/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/r3Cseq", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.r3Cseq", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "MRC WIMM Centre for Computational Biology", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Supat Thongjuea", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "UK", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "University of Oxford", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Weatherall Institute of Molecular Medicine", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:05:49Z", "lastUpdate": "2026-09-01T07:03:31.894678Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "quantsmooth", "description": "Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.", "homepage": "https://bioconductor.org/packages/quantsmooth", "biotoolsID": "quantsmooth", "biotoolsCURIE": "biotools:quantsmooth", "version": [ "1.78.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/quantsmooth_1.78.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/quantsmooth", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.quantsmooth", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Jan Oosting", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Paul Eilers", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Renee Menezes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:04Z", "lastUpdate": "2026-09-01T07:03:21.244131Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "oligo", "description": "A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).", "homepage": "https://bioconductor.org/packages/oligo", "biotoolsID": "oligo", "biotoolsCURIE": "biotools:oligo", "version": [ "1.76.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "LGPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/benilton/oligo", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/oligo", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btq431", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Benilton Carvalho and Rafael Irizarry", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:33Z", "lastUpdate": "2026-09-01T06:59:40.029142Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MLSeq", "description": "This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data.", "homepage": "https://bioconductor.org/packages/MLSeq", "biotoolsID": "mlseq", "biotoolsCURIE": "biotools:mlseq", "version": [ "2.30.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/MLSeq_2.30.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/MLSeq", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.cmpb.2019.04.007", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ahmet Ergun Karaagaoglu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ahmet Ozturk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Dincer Goksuluk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Gokmen Zararsiz", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Izzet Parug Duru", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Selcuk Korkmaz", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Vahap Eldem", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:00:23Z", "lastUpdate": "2026-09-01T06:56:51.941857Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MBttest", "description": "MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.", "homepage": "https://bioconductor.org/packages/MBttest", "biotoolsID": "mbttest", "biotoolsCURIE": "biotools:mbttest", "version": [ "1.40.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/MBttest_1.40.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/MBttest", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.MBttest", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Yuan-De Tan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:51Z", "lastUpdate": "2026-09-01T06:54:25.925355Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MAST", "description": "Methods and models for handling zero-inflated single cell assay data.", "homepage": "https://bioconductor.org/packages/MAST", "biotoolsID": "mast", "biotoolsCURIE": "biotools:mast", "version": [ "1.38.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/RGLab/MAST/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/RGLab/MAST/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/MAST", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.MAST", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Andrew McDavid", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Greg Finak", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Masanao Yajima", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:02:22Z", "lastUpdate": "2026-09-01T06:54:10.730919Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "LymphoSeq", "description": "This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.", "homepage": "https://bioconductor.org/packages/LymphoSeq", "biotoolsID": "lymphoseq", "biotoolsCURIE": "biotools:lymphoseq", "version": [ "1.40.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Windows" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/LymphoSeq_1.40.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/LymphoSeq", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.LymphoSeq", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "David Coffey", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:56:11Z", "lastUpdate": "2026-09-01T06:53:30.849312Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "INSPEcT", "description": "INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data.", "homepage": "https://bioconductor.org/packages/INSPEcT", "biotoolsID": "inspect", "biotoolsCURIE": "biotools:inspect", "version": [ "1.42.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3511", "term": "Nucleic acid sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0099", "term": "RNA" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/INSPEcT_1.42.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/INSPEcT", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv288", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1101/gr.260984.120", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.3389/fgene.2020.00759", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Stefano de Pretis", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:03:35Z", "lastUpdate": "2026-09-01T06:51:15.693594Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "hierGWAS", "description": "Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.", "homepage": "https://bioconductor.org/packages/hierGWAS", "biotoolsID": "hiergwas", "biotoolsCURIE": "biotools:hiergwas", "version": [ "1.42.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Mac", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/hierGWAS_1.42.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/hierGWAS", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.hierGWAS", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Laura Buzdugan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:00:42Z", "lastUpdate": "2026-09-01T06:49:36.986826Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gmapR", "description": "GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.", "homepage": "https://bioconductor.org/packages/gmapR", "biotoolsID": "gmapr", "biotoolsCURIE": "biotools:gmapr", "version": [ "1.54.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1276", "term": "Nucleic acid features" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/gmapR_1.54.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/gmapR", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.gmapR", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Cory Barr", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Michael Lawrence", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Thomas Wu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:33Z", "lastUpdate": "2026-09-01T06:47:54.358681Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GeneMeta", "description": "A collection of meta-analysis tools for analysing high throughput experimental data", "homepage": "https://bioconductor.org/packages/GeneMeta", "biotoolsID": "genemeta", "biotoolsCURIE": "biotools:genemeta", "version": [ "1.84.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/GeneMeta_1.84.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/GeneMeta", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.GeneMeta", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Lara Lusa", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "M. Ruschhaupt", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "R. Gentleman", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:03:18Z", "lastUpdate": "2026-09-01T06:46:17.668809Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gcrma", "description": "Background adjustment using sequence information", "homepage": "https://bioconductor.org/packages/gcrma", "biotoolsID": "gcrma", "biotoolsCURIE": "biotools:gcrma", "version": [ "2.84.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "LGPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/gcrma_2.84.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/gcrma", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.gcrma", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Jean", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Rafael Irizarry with contributions from James MacDonald", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:05:09Z", "lastUpdate": "2026-09-01T06:45:47.180572Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EDIR", "description": "EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.", "homepage": "https://bioconductor.org/packages/EDIRquery", "biotoolsID": "edir", "biotoolsCURIE": "biotools:edir", "version": [ "1.12.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0237", "term": "Repeat sequence analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Library", "Web application", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3676", "term": "Exome sequencing" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python", "Shell", "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/lauravongoc/EDIR", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/EDIRquery_1.12.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/EDIRquery", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btac771", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Laura D.T. Vo Ngoc", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "Chan019", "additionDate": "2023-02-20T16:58:39.212211Z", "lastUpdate": "2026-09-01T06:43:07.935547Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "covRNA", "description": "This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.", "homepage": "https://bioconductor.org/packages/covRNA", "biotoolsID": "covrna", "biotoolsCURIE": "biotools:covrna", "version": [ "1.38.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/covRNA_1.38.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/covRNA", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.covRNA", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Lara Urban", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:03:12Z", "lastUpdate": "2026-09-01T06:38:53.141110Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "codelink", "description": "This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.", "homepage": "https://bioconductor.org/packages/codelink", "biotoolsID": "codelink", "biotoolsCURIE": "biotools:codelink", "version": [ "1.80.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ddiez/codelink", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://github.com/ddiez/codelink", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/codelink", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btm072", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Diego Diez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:20Z", "lastUpdate": "2026-09-01T06:38:02.105434Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CMA", "description": "This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.", "homepage": "https://bioconductor.org/packages/CMA", "biotoolsID": "cma", "biotoolsCURIE": "biotools:cma", "version": [ "1.70.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_2995", "term": "Sequence classification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-2.0-or-later", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/CMA_1.70.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/CMA", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.CMA", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Anne-Laure Boulesteix", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Christoph Bernau", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Martin Slawski", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:00:10Z", "lastUpdate": "2026-09-01T06:37:24.804346Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CGHregions", "description": "Dimension Reduction for Array CGH Data with Minimal Information Loss", "homepage": "https://bioconductor.org/packages/CGHregions", "biotoolsID": "cghregions", "biotoolsCURIE": "biotools:cghregions", "version": [ "1.70.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/CGHregions_1.70.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/CGHregions", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.CGHregions", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Sjoerd Vosse & Mark van de Wiel", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:00:56Z", "lastUpdate": "2026-09-01T06:36:09.025321Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CGHcall", "description": "Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.", "homepage": "https://bioconductor.org/packages/CGHcall", "biotoolsID": "cghcall", "biotoolsCURIE": "biotools:cghcall", "version": [ "2.74.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/CGHcall_2.74.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/CGHcall", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.CGHcall", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Mark van de Wiel", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Sjoerd Vosse", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:05:06Z", "lastUpdate": "2026-09-01T06:36:01.295357Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bigmelon", "description": "Methods for working with Illumina arrays using gdsfmt.", "homepage": "https://bioconductor.org/packages/bigmelon", "biotoolsID": "bigmelon", "biotoolsCURIE": "biotools:bigmelon", "version": [ "1.38.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/bigmelon_1.38.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/bigmelon", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty713", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ayden Saffari", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Karim Malki", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Leonard C. Schalkwyk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Tyler J. Gorrie-Stone", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:01:12Z", "lastUpdate": "2026-09-01T06:32:45.813912Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BBCAnalyzer", "description": "BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.", "homepage": "https://bioconductor.org/packages/BBCAnalyzer", "biotoolsID": "bbcanalyzer", "biotoolsCURIE": "biotools:bbcanalyzer", "version": [ "1.42.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2921", "term": "Sequence variation annotation format" }, { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] }, { "data": { "uri": "http://edamontology.org/data_2166", "term": "Sequence composition plot" }, "format": [ { "uri": "http://edamontology.org/format_2921", "term": "Sequence variation annotation format" }, { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "LGPL-3.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/BBCAnalyzer_1.42.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/BBCAnalyzer", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.BBCAnalyzer", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Sarah Sandmann", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:28Z", "lastUpdate": "2026-09-01T06:32:18.808767Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BaseSpaceR", "description": "A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.", "homepage": "https://bioconductor.org/packages/BaseSpaceR", "biotoolsID": "basespacer", "biotoolsCURIE": "biotools:basespacer", "version": [ "1.56.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3372", "term": "Software engineering" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "R" ], "license": "Apache-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/BaseSpaceR_1.56.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/BaseSpaceR", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.BaseSpaceR", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Adrian Alexa", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:55:06Z", "lastUpdate": "2026-09-01T06:32:05.123991Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bamsignals", "description": "This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.", "homepage": "https://bioconductor.org/packages/bamsignals", "biotoolsID": "bamsignals", "biotoolsCURIE": "biotools:bamsignals", "version": [ "1.44.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/lamortenera/bamsignals", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://bioconductor.org/packages/bamsignals", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.18129/B9.bioc.bamsignals", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Alessandro Mammana", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Johannes Helmuth", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:28Z", "lastUpdate": "2026-09-01T06:31:57.809046Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }