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{ "count": 29521, "next": "?page=2", "previous": null, "list": [ { "name": "hictk", "description": "Blazing fast toolkit to work with .hic and .cool files", "homepage": "https://github.com/paulsengroup/hictk", "biotoolsID": "hictk", "biotoolsCURIE": "biotools:hictk", "version": [ "0.0.1", "0.0.2", "0.0.3", "0.0.4", "0.0.5", "0.0.6", "0.0.7", "0.0.8", "0.0.9", "0.0.10", "0.0.11", "0.0.12" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/paulsengroup/hictk", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/paulsengroup/hictk/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/paulsengroup/hictk/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/hictk", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/paulsengroup/hictk/pkgs/container/hictk", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://hictk.readthedocs.io/en/latest/index.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2023.11.26.568707", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [], "community": null, "owner": "robomics", "additionDate": "2024-02-02T14:42:46.030561Z", "lastUpdate": "2024-04-18T07:26:50.285636Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Single-cell Proteomic DataBase", "description": "Comprehensive resource and knowledgebase for proteomic data at the single-cell resolution.", "homepage": "https://scproteomicsdb.com/", "biotoolsID": "scpdb", "biotoolsCURIE": "biotools:scpdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0820", "term": "Membrane and lipoproteins" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/NAR/GKAD1018", "pmid": "37953313", "pmcid": "PMC10767837", "type": [], "version": null, "note": null, "metadata": { "title": "SPDB:ã comprehensive resourceãnd knowledgebase for proteomic dataãt the single-cell resolution", "abstract": "The single-cell proteomics enables the direct quantification of proteinãbundanceãt the single-cell resolution, providing valuable insights into cellular phenotypes be y ond what can be inferred from transcriptomeãnalysisãlone. However, insufficient large-scale integrated databases hinder researchers fromãccessingãnd exploring single-cell proteomics, impeding theãdvancement of this field. To fill this deficiency, we presentã comprehensive database, namely Single-cell Proteomic DataBase (SPDB, https:// scproteomicsdb.com/ ), for general single-cell proteomic data, includingãntibody-based or mass spectrometry-based single-cell proteomics. Equipped with stãndardized datã processãndã user-friendly web interfãce, SPDB pro vides unified data formats for convenient interaction with downstreamãnalysis,ãnd offers not only dataset-level butãlso protein-le v el data searchãnd exploration capabilities. To enable detailed exhibition of single-cell proteomic data, SPDBãlso providesã module for visualizing data from the perspectives of cell metãdatã or protein features. The current version of SPDB encompasses 133ãntibody-based single-cell proteomic datasets in v olving more than 300 million cellsãnd o v er 800 mark er / surfãce proteins,ãnd 10 mass spectrometry-based single-cell proteomic datasets in v olving more than 40 0 0 cellsãnd o v er 70 0 0 proteins. Ov erall, SPDB is en visioned to be exploredãsã useful resource that will facilitate the wider research communities by providing detailed insights into proteomics from the single-cell perspective.", "date": "2024-01-05T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Wang F." }, { "name": "Liu C." }, { "name": "Li J." }, { "name": "Yang F." }, { "name": "Song J." }, { "name": "Zang T." }, { "name": "Yao J." }, { "name": "Wang G." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jianhua Yao", "email": "jianhuayao@tencent.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Guohua Wang", "email": "ghwang@hit.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T14:45:34.140169Z", "lastUpdate": "2024-04-16T14:45:34.142458Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PhenoSV", "description": "PhenoSV is a phenotype-aware structural variants interpretation and prioritization tool.", "homepage": "https://phenosv.wglab.org", "biotoolsID": "phenosv", "biotoolsCURIE": "biotools:phenosv", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" }, { "uri": "http://edamontology.org/operation_0441", "term": "cis-regulatory element prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41467-023-43651-Y", "pmid": "38016949", "pmcid": "PMC10684511", "type": [], "version": null, "note": null, "metadata": { "title": "PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants", "abstract": "Structural variants (SVs) represent a major source of genetic variation associated with phenotypic diversity and disease susceptibility. While long-read sequencing can discover over 20,000 SVs per human genome, interpreting their functional consequences remains challenging. Existing methods for identifying disease-related SVs focus on deletion/duplication only and cannot prioritize individual genes affected by SVs, especially for noncoding SVs. Here, we introduce PhenoSV, a phenotype-aware machine-learning model that interprets all major types of SVs and genes affected. PhenoSV segments and annotates SVs with diverse genomic features and employs a transformer-based architecture to predict their impacts under a multiple-instance learning framework. With phenotype information, PhenoSV further utilizes gene-phenotype associations to prioritize phenotype-related SVs. Evaluation on extensive human SV datasets covering all SV types demonstrates PhenoSV’s superior performance over competing methods. Applications in diseases suggest that PhenoSV can determine disease-related genes from SVs. A web server and a command-line tool for PhenoSV are available at https://phenosv.wglab.org .", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Xu Z." }, { "name": "Li Q." }, { "name": "Marchionni L." }, { "name": "Wang K." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Kai Wang", "email": "wangk@chop.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-5585-982X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Zhuoran Xu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T14:15:59.343761Z", "lastUpdate": "2024-04-16T14:15:59.346819Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MuDoGeR", "description": "The Multi-Domain Genome Recovery v1.0 (MuDoGeR v1.0) framework is a tool developed to help users to recover Metagenome-Assembled Genomes and Uncultivated Viral Genomes from whole-genome sequence (WGS) samples simultaneously. The MuDoGeR v1.0 framework acts as a wrapper for several tools. It was designed to be an easy-to-use tool that outputs ready-to-use comprehensive files.", "homepage": "https://github.com/mdsufz/MuDoGeR", "biotoolsID": "mudoger", "biotoolsCURIE": "biotools:mudoger", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Shell", "R", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1111/1755-0998.13904", "pmid": "37994269", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy", "abstract": "Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.", "date": "2024-02-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Rocha U." }, { "name": "CoelhoKasmanas J." }, { "name": "Kallies R." }, { "name": "Saraiva J.P." }, { "name": "Toscan R.B." }, { "name": "Stefanic P." }, { "name": "Bicalho M.F." }, { "name": "BorimCorrea F." }, { "name": "Basturk M.N." }, { "name": "Fousekis E." }, { "name": "VianaBarbosa L.M." }, { "name": "Plewka J." }, { "name": "Probst A.J." }, { "name": "Baldrian P." }, { "name": "Stadler P.F." } ], "journal": "Molecular Ecology Resources" } } ], "credit": [ { "name": "Ulisses Rocha", "email": "ulisses.rocha@ufz.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T14:14:05.166974Z", "lastUpdate": "2024-04-16T14:14:05.169036Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "oggmap", "description": "Python package to extract gene ages per orthogroup and link them with single-cell RNA data.", "homepage": "https://github.com/kullrich/oggmap", "biotoolsID": "oggmap", "biotoolsCURIE": "biotools:oggmap", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3935", "term": "Dimensionality reduction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://oggmap.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAD657", "pmid": "37952198", "pmcid": "PMC10663984", "type": [], "version": null, "note": null, "metadata": { "title": "oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data", "abstract": "Summary: For model species, single-cell RNA-based cell atlases are available. A good cell atlas includes all major stages in a species’ ontogeny, and soon, they will be standard even for nonmodel species. Here, we propose a Python package called oggmap, which allows for the easy extraction of an orthomap (gene ages per orthogroup) for any given query species from OrthoFinder and other gene family data resources, like homologous groups from eggNOG or PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic species which can be further used to calculate gene age-weighted expression data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited to one transcriptome evolutionary index, oggmap can visualize the individual gene category (e.g. age class, nucleotide diversity bin) and their corresponding expression profiles to investigate scRNA-based cell type assignments in an evolutionary context.", "date": "2023-11-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Ullrich K.K." }, { "name": "Glytnasi N.E." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Kristian K Ullrich", "email": "ullrich@evolbio.mpg.de", "url": null, "orcidid": "https://orcid.org/0000-0003-4308-9626", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Nikoleta E Glytnasi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T14:10:00.623929Z", "lastUpdate": "2024-04-16T14:10:00.646441Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Cirscan", "description": "Shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks.", "homepage": "https://gitlab.com/geobioinfo/cirscan_Rshiny", "biotoolsID": "cirscan", "biotoolsCURIE": "biotools:cirscan", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-024-05668-y", "pmid": "38302900", "pmcid": "PMC10832221", "type": [], "version": null, "note": null, "metadata": { "title": "Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA–miRNA–mRNA networks", "abstract": "Background: Non-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood. Among non-coding RNAs, circular RNAs (circRNAs) have recently been identified for their microRNA (miRNA) sponge function which allows them to modulate the expression of miRNA target genes by taking on the role of competitive endogenous RNAs (ce-circRNAs). Today, most computational tools are not adapted to the search for ce-circRNAs or have not been developed for the search for ce-circRNAs from user’s transcriptomic data. Results: In this study, we present Cirscan (CIRcular RNA Sponge CANdidates), an interactive Shiny application that automatically infers circRNA–miRNA–mRNA networks from human multi-level transcript expression data from two biological conditions (e.g. tumor versus normal conditions in the case of cancer study) in order to identify on a large scale, potential sponge mechanisms active in a specific condition. Cirscan ranks each circRNA–miRNA–mRNA subnetwork according to a sponge score that integrates multiple criteria based on interaction reliability and expression level. Finally, the top ranked sponge mechanisms can be visualized as networks and an enrichment analysis is performed to help its biological interpretation. We showed on two real case studies that Cirscan is capable of retrieving sponge mechanisms previously described, as well as identifying potential novel circRNA sponge candidates. Conclusions: Cirscan can be considered as a companion tool for biologists, facilitating their ability to prioritize sponge mechanisms for experimental validations and identifying potential therapeutic targets. Cirscan is implemented in R, released under the license GPL-3 and accessible on GitLab (https://gitlab.com/geobioinfo/cirscan_Rshiny ). The scripts used in this paper are also provided on Gitlab (https://gitlab.com/geobioinfo/cirscan_paper ).", "date": "2024-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Fraboulet R.-M." }, { "name": "Si Ahmed Y." }, { "name": "Aubry M." }, { "name": "Corre S." }, { "name": "Galibert M.-D." }, { "name": "Blum Y." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Yuna Blum", "email": "yuna.blum@univ-rennes.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Rose-Marie Fraboulet", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T14:03:57.384386Z", "lastUpdate": "2024-04-16T14:05:09.344226Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "RecView", "description": "This R package is designed to distribute the RecView ShinyApp which aims at providing a user-friendly GUI for viewing and locating recombination positions on chromosomes using pedigree data.", "homepage": "https://github.com/HKyleZhang/RecView.git", "biotoolsID": "recview", "biotoolsCURIE": "biotools:recview", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_0451", "term": "Recombination detection" }, { "uri": "http://edamontology.org/operation_0484", "term": "SNP detection" }, { "uri": "http://edamontology.org/operation_0282", "term": "Genetic mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3127", "term": "DNA replication and recombination" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/S12864-023-09807-2", "pmid": "38007417", "pmcid": "PMC10676570", "type": [], "version": null, "note": null, "metadata": { "title": "RecView: an interactive R application for locating recombination positions using pedigree data", "abstract": "Background: Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes. Results: We present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions. Conclusions: RecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub (https://github.com/HKyleZhang/RecView.git).", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Zhang H." }, { "name": "Hansson B." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Hongkai Zhang", "email": "hongkai.zhang@biol.lu.se", "url": null, "orcidid": "https://orcid.org/0000-0001-7371-9612", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Bengt Hansson", "email": "bengt.hansson@biol.lu.se", "url": null, "orcidid": "https://orcid.org/0000-0001-6694-8169", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T14:01:37.903804Z", "lastUpdate": "2024-04-16T14:01:37.906051Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "STOmicsDB", "description": "Comprehensive database for spatial transcriptomics data sharing, analysis and visualization.", "homepage": "https://db.cngb.org/stomics/", "biotoolsID": "stomicsdb", "biotoolsCURIE": "biotools:stomicsdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://stomics-data-archive.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/NAR/GKAD933", "pmid": "37953328", "pmcid": "PMC10767841", "type": [], "version": null, "note": null, "metadata": { "title": "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization", "abstract": "Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their spatial locations at the single-cell level, generating detailed biological insight into biological processes. A comprehensive database could facilitate the sharing of spatial transcriptomic data and streamline the data acquisition process for researchers. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified spatial regions and genes, and performed cell-cell interaction analysis for these datasets. STOmicsDB features a user-friendly interface for the rapid visualization of millions of cells. To further facilitate the reusability and interoperability of spatial transcriptomic data, we developed standards for spatial transcriptomic data archiving and constructed a spatial transcriptomic data archiving system. Additionally, we offer a distinctive capability of customizing dedicated sub-databases in STOmicsDB for researchers, assisting them in visualizing their spatial transcriptomic analyses. We believe that STOmicsDB could contribute to research insights in the spatial transcriptomics field, including data archiving, sharing, visualization and analysis. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.", "date": "2024-01-05T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Xu Z." }, { "name": "Wang W." }, { "name": "Yang T." }, { "name": "Li L." }, { "name": "Ma X." }, { "name": "Chen J." }, { "name": "Wang J." }, { "name": "Huang Y." }, { "name": "Gould J." }, { "name": "Lu H." }, { "name": "Du W." }, { "name": "Sahu S.K." }, { "name": "Yang F." }, { "name": "Li Z." }, { "name": "Hu Q." }, { "name": "Hua C." }, { "name": "Hu S." }, { "name": "Liu Y." }, { "name": "Cai J." }, { "name": "You L." }, { "name": "Zhang Y." }, { "name": "Li Y." }, { "name": "Zeng W." }, { "name": "Chen A." }, { "name": "Wang B." }, { "name": "Liu L." }, { "name": "Chen F." }, { "name": "Ma K." }, { "name": "Xu X." }, { "name": "Wei X." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Kailong Ma", "email": "makailong@cngb.org", "url": null, "orcidid": "https://orcid.org/0000-0002-9351-104X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xun Xu", "email": "xuxun@genomics.cn", "url": null, "orcidid": "https://orcid.org/0000-0002-5338-5173", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xiaofeng Wei", "email": "weixiaofeng@cngb.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T10:56:15.558018Z", "lastUpdate": "2024-04-16T10:56:15.560225Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MLpronto", "description": "MLpronto is a tool for rapid, robust, and reproducible machine learning. No ML background is needed whatsoever.", "homepage": "https://mlpronto.org/", "biotoolsID": "mlpronto", "biotoolsCURIE": "biotools:mlpronto", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3659", "term": "Regression analysis" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3372", "term": "Software engineering" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/btjaden/MLpronto", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1371/JOURNAL.PONE.0294924", "pmid": "38032968", "pmcid": "PMC10688639", "type": [], "version": null, "note": null, "metadata": { "title": "MLpronto: A tool for democratizing machine learning", "abstract": "The democratization of machine learning is a popular and growing movement. In a world with a wealth of publicly available data, it is important that algorithms for analysis of data are accessible and usable by everyone. We present MLpronto, a system for machine learning analysis that is designed to be easy to use so as to facilitate engagement with machine learning algorithms. With its web interface, MLpronto requires no computer programming or machine learning background, and it normally returns results in a matter of seconds. As input, MLpronto takes a file of data to be analyzed. MLpronto then executes some of the more commonly used supervised machine learning algorithms on the data and reports the results of the analyses. As part of its execution, MLpronto generates computer programming code corresponding to its machine learning analysis, which it also supplies as output. Thus, MLpronto can be used as a no-code solution for citizen data scientists with no machine learning or programming background, as an educational tool for those learning about machine learning, and as a first step for those who prefer to engage with programming code in order to facilitate rapid development of machine learning projects. MLpronto is freely available for use at https://mlpronto.org/.", "date": "2023-11-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Tjaden J." }, { "name": "Tjaden B." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Brian Tjaden", "email": "btjaden@wellesley.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jacob Tjaden", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-04-16T10:54:23.655728Z", "lastUpdate": "2024-04-16T10:54:23.657995Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BCFtools", "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.", "homepage": "http://www.htslib.org/", "biotoolsID": "bcftools", "biotoolsCURIE": "biotools:bcftools", "version": [ "1.0", "1.1", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.20" ], "otherID": [], "relation": [ { "biotoolsID": "htslib", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "note": "Multiple data munging operations.", "cmd": null } ], "toolType": [ "Command-line tool", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_3516", "term": "Genotyping experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "BCFtools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/bcftools", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/bcftools/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/bcftools.html", "type": [ "General" ], "note": null }, { "url": "http://www.htslib.org/workflow/#mapping_to_variant", "type": [ "Other" ], "note": "A workflow for BCFtools." } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": "19505943", "pmcid": "PMC2723002", "type": [ "Primary" ], "version": null, "note": "The Sequence Alignment/Map format and SAMtools.", "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 37126, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.", "date": "2021-02-01T00:00:00Z", "citationCount": 3084, "authors": [ { "name": "Danecek P." }, { "name": "Bonfield J.K." }, { "name": "Liddle J." }, { "name": "Marshall J." }, { "name": "Ohan V." }, { "name": "Pollard M.O." }, { "name": "Whitwham A." }, { "name": "Keane T." }, { "name": "McCarthy S.A." }, { "name": "Davies R.M." } ], "journal": "GigaScience" } } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "community": null, "owner": "awhitwham", "additionDate": "2015-08-24T08:35:55Z", "lastUpdate": "2024-04-16T10:25:06.228249Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }