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{ "count": 2071, "next": "?page=2", "previous": null, "list": [ { "name": "metabuli", "description": "Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid", "homepage": "https://metabuli.steineggerlab.com", "biotoolsID": "metabuli", "biotoolsCURIE": "biotools:metabuli", "version": [], "otherID": [], "relation": [ { "biotoolsID": "mmseqs2", "type": "uses" }, { "biotoolsID": "gtdb", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/steineggerlab/Metabuli/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/steineggerlab/Metabuli", "type": [ "Repository" ], "note": "github repository" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/s41592-024-02273-y", "pmid": "38769467", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "milot-mirdita", "additionDate": "2023-06-07T03:22:25.847061Z", "lastUpdate": "2026-02-12T14:21:25.897853Z", "editPermission": { "type": "group", "authors": [ "vashokan" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "decompTumor2Sig", "description": "R package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.", "homepage": "http://rmpiro.net/decompTumor2Sig/", "biotoolsID": "decompTumor2Sig", "biotoolsCURIE": "biotools:decompTumor2Sig", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/rmpiro/decompTumor2Sig", "type": [ "Repository" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://rmpiro.net/index.html#downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-019-2688-6", "pmid": "30999866", "pmcid": "PMC6472187", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DecompTumor2Sig: Identification of mutational signatures active in individual tumors", "abstract": "© 2019 The Author(s).Background: The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic processes like age-related spontaneous deamination of 5-methylcytosine. The effect of such mutational processes can be modeled by mutational signatures, of which two different conceptualizations exist: the model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial identification and definition of mutational signatures requires large sets of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use R package that can decompose an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor. Until now, such tools were available only for Alexandrov signatures. We demonstrate the correctness and usefulness of our approach with three test cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor genomes of ten different tumor entities, and from simulated tumor genomes, respectively. Conclusions: The decompTumor2Sig package is freely available and has been accepted for inclusion in Bioconductor.", "date": "2019-04-18T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Kruger S." }, { "name": "Piro R.M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Prof. Dr. Rosario M. Piro", "email": "r.piro@fu-berlin.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "Ruta", "additionDate": "2019-06-20T14:18:28Z", "lastUpdate": "2026-02-02T08:12:42.981321Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-POLIMI" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pantas", "description": "Differential quantification of alternative splicing events on spliced pangenome graphs.", "homepage": "https://github.com/algolab/pantas", "biotoolsID": "pantas", "biotoolsCURIE": "biotools:pantas", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3320", "term": "RNA splicing" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/AlgoLab/pantas", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/AlgoLab/pantas/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/AlgoLab/pantas", "type": "Source code", "note": null, "version": null }, { "url": "https://hub.docker.com/r/algolab/pantas", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/AlgoLab/pantas/blob/main/README.md", "type": [ "General", "Installation instructions", "Quick start guide", "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1012665", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "yp", "additionDate": "2026-01-30T22:36:14.902508Z", "lastUpdate": "2026-01-30T22:36:14.904749Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RecGraph", "description": "RecGraph is a tool for computing optimal sequence-to-graph alignment with recombinations.", "homepage": "https://github.com/AlgoLab/RecGraph", "biotoolsID": "recgraph", "biotoolsCURIE": "biotools:recgraph", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3796", "term": "Population genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Rust" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": null, "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/AlgoLab/RecGraph", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/AlgoLab/RecGraph/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/AlgoLab/RecGraph/releases/tag/v1.0.0", "type": "Binaries", "note": null, "version": "1.0.0" }, { "url": "https://anaconda.org/channels/bioconda/packages/recgraph/overview", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/AlgoLab/RecGraph/blob/main/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btae292", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "1.0.0", "note": null, "metadata": null } ], "credit": [], "owner": "yp", "additionDate": "2026-01-27T17:11:15.880698Z", "lastUpdate": "2026-01-30T22:07:27.044664Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bakta", "description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", "homepage": "https://github.com/oschwengers/bakta", "biotoolsID": "bakta", "biotoolsCURIE": "biotools:bakta", "version": [ "v1.12.0" ], "otherID": [], "relation": [ { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "hmmer3", "type": "uses" }, { "biotoolsID": "infernal", "type": "uses" }, { "biotoolsID": "trnascan-se", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "aragorn", "type": "uses" }, { "biotoolsID": "pilercr", "type": "uses" }, { "biotoolsID": "deepsig", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2914", "term": "Sequence features metadata" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [ { "uri": "http://edamontology.org/format_3329", "term": "HMMER3" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1975", "term": "GFF3" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta" } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/oschwengers/bakta", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://bioconda.github.io/recipes/bakta/README.html", "type": [ "Other" ], "note": null }, { "url": "https://bakta.computational.bio", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://zenodo.org/records/14916843", "type": "Other", "note": "Mandatory annotation database", "version": "v6.0" } ], "documentation": [ { "url": "https://github.com/oschwengers/bakta/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md", "type": [ "Contributions policy" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://bakta.readthedocs.io/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1099/mgen.0.000685", "pmid": "34739369", "pmcid": "PMC8743544", "type": [ "Primary" ], "version": "1.1", "note": null, "metadata": null }, { "doi": "10.1093/nar/gkaf335", "pmid": "40271661", "pmcid": "PMC12230652", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Oliver Schwengers", "email": "oliver.schwengers@cb.jlug.de", "url": "https://github.com/oschwengers", "orcidid": "https://orcid.org/0000-0003-4216-2721", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Justus Liebig University Giessen", "email": null, "url": "https://www.uni-giessen.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "oschwengers", "additionDate": "2021-05-08T17:25:21Z", "lastUpdate": "2026-01-29T12:11:19.042627Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "bebatut" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "iCodon", "description": "iCodon is a tool for ideal codon design for customized gene expression.", "homepage": "https://bazzinilab.shinyapps.io/icodon/", "biotoolsID": "icodon", "biotoolsCURIE": "biotools:icodon", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3095", "term": "Nucleic acid design" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_0441", "term": "cis-regulatory element prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/santiago1234/iCodon", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/santiago1234/iCodon/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2021.05.06.442969", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ariel Alejandro Bazzini", "email": "arb@stowers.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-09-27T07:31:29.303373Z", "lastUpdate": "2026-01-28T15:28:03.870976Z", "editPermission": { "type": "group", "authors": [ "jian" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "kraken2", "description": "Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.\nAny assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”)", "homepage": "https://github.com/DerrickWood/kraken2", "biotoolsID": "kraken2", "biotoolsCURIE": "biotools:kraken2", "version": [ "2.0.8-beta" ], "otherID": [], "relation": [ { "biotoolsID": "kraken", "type": "isNewVersionOf" }, { "biotoolsID": "bracken", "type": "usedBy" }, { "biotoolsID": "gtdb", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "`kraken2 --db <kraken2_database> <input.fastq>`" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" } ], "operatingSystem": [], "language": [ "Perl", "C++" ], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/DerrickWood/kraken2", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/DerrickWood/kraken2/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/DerrickWood/kraken2/archive/v2.0.8-beta.tar.gz", "type": "Source code", "note": null, "version": "2.0.8-beta" } ], "documentation": [ { "url": "https://github.com/DerrickWood/kraken2/wiki/Manual", "type": [ "User manual" ], "note": null }, { "url": "https://benlangmead.github.io/aws-indexes/k2", "type": [ "User manual" ], "note": "Links to multiple Kraken 2 and bracken databases and indexes" } ], "publication": [ { "doi": "10.1101/762302", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Derrick E. 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pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ElucidataInc/ElMaven", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ElucidataInc/ElMaven/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://elucidatainc.github.io/ElMaven/Downloads/", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/ElucidataInc/ElMaven/releases", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://elucidatainc.github.io/ElMaven/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-9236-2_19", "pmid": "31119671", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing engine for metabolomics", "abstract": "", "date": "2019-01-01T00:00:00Z", "citationCount": 106, "authors": [], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": null, "email": "info@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "elmaven@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:14:25Z", "lastUpdate": "2025-11-03T16:47:19.388844Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CliqueMS", "description": "Computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.", "homepage": "https://github.com/osenan/cliqueMS", "biotoolsID": "CliqueMS", "biotoolsCURIE": "biotools:CliqueMS", "version": [ "0.3.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3798", "term": "Read binning" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R", "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/osenan/cliqueMS/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://cran.r-project.org/src/contrib/Archive/cliqueMS/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/osenan/cliqueMS/blob/master/vignettes/annotate_features.Rmd", "type": [ "Training material" ], "note": "Tutorial material" } ], "publication": [ { "doi": "10.1093/bioinformatics/btz207", "pmid": "30903689", "pmcid": "PMC6792096", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "CliqueMS: A computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network", "abstract": "The analysis of biological samples in untargeted metabolomic studies using LC-MS yields tens of thousands of ion signals. Annotating these features is of the utmost importance for answering questions as fundamental as, e.g. how many metabolites are there in a given sample.Results: Here, we introduce CliqueMS, a new algorithm for annotating in-source LC-MS1 data. CliqueMS is based on the similarity between coelution profiles and therefore, as opposed to most methods, allows for the annotation of a single spectrum. Furthermore, CliqueMS improves upon the state of the art in several dimensions: (i) it uses a more discriminatory feature similarity metric; (ii) it treats the similarities between features in a transparent way by means of a simple generativemodel; (iii) it uses a well-grounded maximum likelihood inference approach to group features; (iv) it uses empirical adduct frequencies to identify the parental mass and (v) it deals more flexibly with the identification of the parental mass by proposing and ranking alternative annotations. We validate our approach with simple mixtures of standards and with real complex biological samples. CliqueMS reduces the thousands of features typically obtained in complex samples to hundreds of metabolites, and it is able to correctly annotate more metabolites and adducts from a single spectrum than available tools.", "date": "2019-10-15T00:00:00Z", "citationCount": 48, "authors": [ { "name": "Senan O." }, { "name": "Aguilar-Mogas A." }, { "name": "Navarro M." }, { "name": "Capellades J." }, { "name": "Noon L." }, { "name": "Burks D." }, { "name": "Yanes O." }, { "name": "Guimera R." }, { "name": "Sales-Pardo M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Oriol Senan", "email": "oriol.senan@urv.cat", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Ruta", "additionDate": "2019-07-04T14:05:39Z", "lastUpdate": "2025-11-03T16:44:03.166147Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "The MINERVA Platform", "description": "The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. 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"Hakim Achterberg", "email": "h.achterberg@erasmusmc.nl", "url": "https://bigr.nl/member/hakim/", "orcidid": "https://orcid.org/0000-0003-3772-4582", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Erasmus MC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "hachterberg", "additionDate": "2025-07-23T10:24:09.622930Z", "lastUpdate": "2025-07-24T08:55:06.000976Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "InMoose", "description": "InMoose, the INtegrated Multi-Omic Open-Source environment, ports to Python state-of-the-art R tools for the analysis of transcriptomic data.", "homepage": "https://github.com/epigenelabs/inmoose", "biotoolsID": "inmoose", "biotoolsCURIE": "biotools:inmoose", "version": [ "0.8.0" ], "otherID": [], "relation": [ { "biotoolsID": "deseq2", "type": "isNewVersionOf" }, { "biotoolsID": "limma", "type": "isNewVersionOf" }, { "biotoolsID": "edger", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/epigenelabs/inmoose", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/epigenelabs/inmoose/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://inmoose.readthedocs.io/en/stable/", "type": [ "General" ], "note": null }, { "url": "https://colab.research.google.com/drive/1bzmNDZeaw1A6tSgfx61O6PFtaQDve6SV?usp=sharing", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1038/s41598-025-03376-y", "pmid": null, "pmcid": null, "type": [ "Primary", "Usage" ], "version": null, "note": null, "metadata": { "title": "Bridging the gap between R and Python in bulk transcriptomic data analysis with InMoose", "abstract": "We introduce InMoose, an open-source Python environment aimed at omic data analysis. We illustrate its capabilities for bulk transcriptomic data analysis. Due to its wide adoption, Python has grown as a de facto standard in fields increasingly important for bioinformatic pipelines, such as data science, machine learning, or artificial intelligence (AI). As a general-purpose language, Python is also recognized for its versatility and scalability. InMoose aims at bringing state-of-the-art tools, historically written in R, to the Python ecosystem. InMoose focuses on providing drop-in replacements for R tools, to ensure consistency and reproducibility between R-based and Python-based pipelines. The first development phase has focused on bulk transcriptomic data, with current capabilities encompassing data simulation, batch effect correction, and differential analysis and meta-analysis.", "date": "2025-12-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Colange M." }, { "name": "Appe G." }, { "name": "Meunier L." }, { "name": "Weill S." }, { "name": "Johnson W.E." }, { "name": "Nordor A." }, { "name": "Behdenna A." } ], "journal": "Scientific Reports" } }, { "doi": "10.1186/s12859-023-05578-5", "pmid": null, "pmcid": null, "type": [ "Benchmarking study", "Method" ], "version": null, "note": null, "metadata": { "title": "pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods", "abstract": "Background: Variability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical biases, called batch effects, in, respectively, microarray and RNA-Seq expression data. Results: In this technical note, we present a new Python implementation of ComBat and ComBat-Seq. While the mathematical framework is strictly the same, we show here that our implementations: (i) have similar results in terms of batch effects correction; (ii) are as fast or faster than the original implementations in R and; (iii) offer new tools for the bioinformatics community to participate in its development. pyComBat is implemented in the Python language and is distributed under GPL-3.0 (https://www.gnu.org/licenses/gpl-3.0.en.html) license as a module of the inmoose package. Source code is available at https://github.com/epigenelabs/inmoose and Python package at https://pypi.org/project/inmoose . Conclusions: We present a new Python implementation of state-of-the-art tools ComBat and ComBat-Seq for the correction of batch effects in microarray and RNA-Seq data. This new implementation, based on the same mathematical frameworks as ComBat and ComBat-Seq, offers similar power for batch effect correction, at reduced computational cost.", "date": "2023-12-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Behdenna A." }, { "name": "Colange M." }, { "name": "Haziza J." }, { "name": "Gema A." }, { "name": "Appe G." }, { "name": "Azencott C.-A." }, { "name": "Nordor A." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1186/s12859-025-06180-7", "pmid": null, "pmcid": null, "type": [ "Benchmarking study", "Method" ], "version": null, "note": null, "metadata": { "title": "Differential expression analysis with inmoose, the integrated multi-omic open-source environment in Python", "abstract": "Background: Differential gene expression analysis is a prominent technique for the analysis of biomolecular data to identify genetic features associated with phenotypes. Limma—for microarray data –, and edgeR and DESeq2—for RNA-Seq data–, are the most widely used tools for differential gene expression analysis of bulk transcriptomic data. Results: We present the differential expression features of InMoose, a Python implementation of R tools limma, edgeR, and DESeq2. We experimentally show that InMoose stands as a drop-in replacement for those tools, with nearly identical results. This ensures reproducibility when interfacing both languages in bioinformatic pipelines. InMoose is an open source software released under the GPL3 license, available at www.github.com/epigenelabs/inmoose and https://inmoose.readthedocs.io. Conclusions: We present a new Python implementation of state-of-the-art tools limma, edgeR, and DESeq2, to perform differential gene expression analysis of bulk transcriptomic data. This new implementation exhibits results nearly identical to the original tools, improving interoperability and reproducibility between Python and R bioinformatics pipelines.", "date": "2025-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Colange M." }, { "name": "Appe G." }, { "name": "Meunier L." }, { "name": "Weill S." }, { "name": "Nordor A." }, { "name": "Behdenna A." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Maximilien Colange", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4769-3302", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Epigene Labs", "email": null, "url": "https://www.epigenelabs.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "maximilien.colange", "additionDate": "2025-07-10T12:32:00.838316Z", "lastUpdate": "2025-07-10T13:00:37.310588Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ColoPola dataset for colorectal cancer detection", "description": "The dataset consists of 572 slices (specimens) with 20,592 images. There are 284 cancer samples and 288 normal samples. The lists of samples for training (train+val) set and testing set are provided in the Zenodo repository. Source code in Github is to train and validate five deep learning models using ColoPola dataset.", "homepage": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset", "biotoolsID": "colopola_dataset_for_colorectal_cancer_detection", "biotoolsCURIE": "biotools:colopola_dataset_for_colorectal_cancer_detection", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" } ], "operatingSystem": [ "Windows" ], "language": [ "Python" ], "license": "CC0-1.0", "collectionID": [ "Dataset" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset", "type": [ "Repository" ], "note": "Source code" }, { "url": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset", "type": "Source code", "note": "Python language", "version": "1.0" }, { "url": "https://zenodo.org/records/10554304", "type": "Test data", "note": "Dataset for running source code", "version": "1.2" } ], "documentation": [], "publication": [], "credit": [], "owner": "haile", "additionDate": "2025-07-10T03:21:50.923918Z", "lastUpdate": "2025-07-10T03:33:52.616431Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COPASI", "description": "Open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others. It includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.", "homepage": "http://copasi.org/", "biotoolsID": "copasi", "biotoolsCURIE": "biotools:copasi", "version": [], "otherID": [], "relation": [ { "biotoolsID": "corc", "type": "usedBy" }, { "biotoolsID": "pycotools", "type": "usedBy" }, { "biotoolsID": "biosimulations", "type": "includedIn" }, { "biotoolsID": "sbmlwebapp", "type": "usedBy" }, { "biotoolsID": "libsbml", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3562", "term": "Network simulation" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" }, { "uri": "http://edamontology.org/operation_3926", "term": "Pathway visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3239", "term": "CopasiML" }, { "uri": "http://edamontology.org/format_3685", "term": "SED-ML" }, { "uri": "http://edamontology.org/format_3686", "term": "COMBINE OMEX" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3239", "term": "CopasiML" }, { "uri": "http://edamontology.org/format_3685", "term": "SED-ML" }, { "uri": "http://edamontology.org/format_3686", "term": "COMBINE OMEX" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": "Artistic-2.0", "collectionID": [ "de.NBI", "EBI Training Tools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://groups.google.com/g/copasi-user-forum", "type": [ "Discussion forum" ], "note": "User Forum" }, { "url": "http://tracker.copasi.org/", "type": [ "Issue tracker" ], "note": "Issue tracker" }, { "url": "https://github.com/copasi/COPASI", "type": [ "Repository" ], "note": "Github Repo" }, { "url": "https://fosstodon.org/@copasi", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "http://copasi.org/Download/", "type": "Binaries", "note": "Source and binary packages are available for download.", "version": null } ], "documentation": [ { "url": "http://copasi.org/Support/User_Manual/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btl485", "pmid": "17032683", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "COPASI - A COmplex PAthway SImulator", "abstract": "Motivation: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. Results: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. © 2006 Oxford University Press.", "date": "2006-12-15T00:00:00Z", "citationCount": 2004, "authors": [ { "name": "Hoops S." }, { "name": "Gauges R." }, { "name": "Lee C." }, { "name": "Pahle J." }, { "name": "Simus N." }, { "name": "Singhal M." }, { "name": "Xu L." }, { "name": "Mendes P." }, { "name": "Kummer U." } ], "journal": "Bioinformatics" } }, { "doi": "10.1007/978-1-59745-525-1_2", "pmid": "19399433", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Computational modeling of biochemical networks using COPASI", "abstract": "Computational modeling and simulation of biochemical networks is at the core of systems biology and this includes many types of analyses that can aid understanding of how these systems work. COPASI is a generic software package for modeling and simulation of biochemical networks which provides many of these analyses in convenient ways that do not require the user to program or to have deep knowledge of the numerical algorithms. Here we provide a description of how these modeling techniques can be applied to biochemical models using COPASI. The focus is both on practical aspects of software usage as well as on the utility of these analyses in aiding biological understanding. Practical examples are described for steady-state and time-course simulations, stoichiometric analyses, parameter scanning, sensitivity analysis (including metabolic control analysis), global optimization, parameter estimation, and stochastic simulation. The examples used are all published models that are available in the BioModels database in SBML format. © 2009 Humana Press.", "date": "2009-12-01T00:00:00Z", "citationCount": 171, "authors": [ { "name": "Mendes P." }, { "name": "Hoops S." }, { "name": "Sahle S." }, { "name": "Gauges R." }, { "name": "Dada J." }, { "name": "Kummer U." } ], "journal": "Methods in Molecular Biology" } }, { "doi": "10.1016/j.jbiotec.2017.06.1200", "pmid": "28655634", "pmcid": "PMC5623632", "type": [], "version": null, "note": null, "metadata": { "title": "COPASI and its applications in biotechnology", "abstract": "COPASI is software used for the creation, modification, simulation and computational analysis of kinetic models in various fields. It is open-source, available for all major platforms and provides a user-friendly graphical user interface, but is also controllable via the command line and scripting languages. These are likely reasons for its wide acceptance. We begin this review with a short introduction describing the general approaches and techniques used in computational modeling in the biosciences. Next we introduce the COPASI package, and its capabilities, before looking at typical applications of COPASI in biotechnology.", "date": "2017-11-10T00:00:00Z", "citationCount": 81, "authors": [ { "name": "Bergmann F.T." }, { "name": "Hoops S." }, { "name": "Klahn B." }, { "name": "Kummer U." }, { "name": "Mendes P." }, { "name": "Pahle J." }, { "name": "Sahle S." } ], "journal": "Journal of Biotechnology" } } ], "credit": [ { "name": null, "email": null, "url": "http://copasi.org/About/Team/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Frank T. Bergmann", "email": "frank.bergmann@bioquant.uni-heidelberg.de", "url": null, "orcidid": "https://orcid.org/0000-0001-5553-4702", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "frankbergmann", "additionDate": "2017-01-17T15:07:47Z", "lastUpdate": "2025-07-07T11:17:37.638447Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "purge_dups", "description": "Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences", "homepage": "https://github.com/dfguan/purge_dups", "biotoolsID": "purge_dups", "biotoolsCURIE": "biotools:purge_dups", "version": [ "v.1.2.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3798", "term": "Read binning" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "C" ], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/dfguan/purge_dups", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/dfguan/purge_dups/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/729962", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Dengfeng Guan", "email": null, "url": "https://www.chatlink.com.cn", "orcidid": "https://orcid.org/0000-0002-6376-3940", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2019-11-14T18:08:10Z", "lastUpdate": "2025-06-30T15:34:51.626796Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Compleasm", "description": "Compleasm: a faster and more accurate reimplementation of BUSCO.\nIt provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.", "homepage": "https://github.com/huangnengCSU/compleasm", "biotoolsID": "compleasm", "biotoolsCURIE": "biotools:compleasm", "version": [ "v.0.2.5" ], "otherID": [], "relation": [ { "biotoolsID": "busco", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] } ], "note": "Runs compleasm using the BUSCO set corresponding to the lineage given.", "cmd": "compleasm run -l \"$lineage\" -a assembly.fa -o output_prefix" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/huangnengCSU/compleasm", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/huangnengCSU/compleasm/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://busco.ezlab.org/list_of_lineages.html", "type": [ "Other" ], "note": "List of accepted lineages (taxonomic groups with curated BUSCO sets)" } ], "download": [], "documentation": [ { "url": "https://github.com/huangnengCSU/compleasm/blob/0.2.6/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btad595", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "compleasm: a faster and more accurate reimplementation of BUSCO", "abstract": "Motivation: Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. Results: Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO's 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13.", "date": "2023-10-01T00:00:00Z", "citationCount": 95, "authors": [ { "name": "Huang N." }, { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Neng Huang", "email": "neng@ds.dfci.harvard.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-7187-0749", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "rlibouban", "additionDate": "2024-03-18T14:51:49.667412Z", "lastUpdate": "2025-06-30T15:30:41.266812Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NanoPlot", "description": "NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences", "homepage": "https://github.com/wdecoster/NanoPlot", "biotoolsID": "nanoplot", "biotoolsCURIE": "biotools:nanoplot", "version": [ "v.1.42.0" ], "otherID": [], "relation": [ { "biotoolsID": "nanopack", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" }, { "uri": "http://edamontology.org/operation_2943", "term": "Box-Whisker plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" }, { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wdecoster/NanoPlot", "type": [ "Repository" ], "note": "Issue tracker and most up to date software version" }, { "url": "http://nanoplot.bioinf.be/", "type": [ "Service" ], "note": "Web service with more limited options compared to the command line tool" } ], "download": [ { "url": "https://anaconda.org/bioconda/nanoplot", "type": "Command-line specification", "note": null, "version": null }, { "url": "https://pypi.org/project/NanoPlot/", "type": "Command-line specification", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/wdecoster/NanoPlot", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty149", "pmid": "29547981", "pmcid": "PMC6061794", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "NanoPack: Visualizing and processing long-read sequencing data", "abstract": "Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.", "date": "2018-08-01T00:00:00Z", "citationCount": 1840, "authors": [ { "name": "De Coster W." }, { "name": "D'Hert S." }, { "name": "Schultz D.T." }, { "name": "Cruts M." }, { "name": "Van Broeckhoven C." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Wouter De Coster", "email": null, "url": "https://gigabaseorgigabyte.wordpress.com/", "orcidid": "https://orcid.org/0000-0002-5248-8197", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "wdecoster", "additionDate": "2021-07-06T20:27:27Z", "lastUpdate": "2025-06-18T12:31:48.762608Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NextDenovo", "description": "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a \"correct-then-assemble\" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.", "homepage": "https://github.com/Nextomics/NextDenovo", "biotoolsID": "nextdenovo", "biotoolsCURIE": "biotools:nextdenovo", "version": [ "v.2.5.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_2561", "term": "Sequence assembly format (text)" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [], "language": [ "Python", "C" ], "license": "GPL-3.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Nextomics/NextDenovo/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/Nextomics/NextDenovo/releases/tag/2.5.2", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://nextdenovo.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2023.03.09.531669.", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Nextomics", "email": "support@nextomics.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T21:13:32Z", "lastUpdate": "2025-06-18T12:20:23.607241Z", "editPermission": { "type": "group", "authors": [ "jw", "ELIXIR-CZ", "Keiler_Collier" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
