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{ "count": 30539, "next": "?page=2", "previous": null, "list": [ { "name": "MetaboLink", "description": "A web application for Streamlined Processing and Analysis of Large-Scale Untargeted Metabolomics Data.", "homepage": "https://computproteomics.bmb.sdu.dk/MetaboLink/", "biotoolsID": "metabolink", "biotoolsCURIE": "biotools:metabolink", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "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_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipidomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/M3Metabolomics/MetaboLink/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/M3Metabolomics/MetaboLink/wiki", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAE459", "pmid": "39018180", "pmcid": "PMC11269424", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data", "abstract": "", "date": "2024-07-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Ana Mendes", "email": "anamendesml@outlook.com", "url": null, "orcidid": "https://orcid.org/0009-0008-5170-0927", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Nils J Færgeman", "email": "nils.f@bmb.sdu.dk", "url": null, "orcidid": "https://orcid.org/0000-0002-9281-5287", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2025-07-21T09:43:28.406602Z", "lastUpdate": "2025-09-16T08:41:00.482475Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "navpa", "description": "Navpa is non-software, deriving its name from nav pa', Klingon for paper town. 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Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.", "metadata": { "title": "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes", "abstract": "", "date": "2019-03-01T00:00:00Z", "citationCount": 123, "authors": [], "journal": "Molecular Ecology Resources" } }, { "doi": "10.1101/2025.08.07.669155", "pmid": "40832315", "pmcid": "PMC12363870", "type": [ "Primary" ], "version": "5.0", "note": "BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.669155", "metadata": null }, { "doi": "10.1086/723601", "pmid": "37130229", "pmcid": "PMC10793872", "type": [ "Primary" ], "version": "4.0", "note": "B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. 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"abstract": "", "date": "2023-01-06T00:00:00Z", "citationCount": 35, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/database/bav068", "pmid": "26209309", "pmcid": "PMC4513696", "type": [], "version": "0", "note": null, "metadata": { "title": "Human metabolic atlas: An online resource for human metabolism", "abstract": "", "date": "2015-01-01T00:00:00Z", "citationCount": 66, "authors": [], "journal": "Database" } } ], "credit": [ { "name": "Mihail Anton", "email": "contact@metabolicatlas.org", "url": null, "orcidid": "https://orcid.org/0000-0002-7753-9042", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "M", "additionDate": "2020-04-23T07:50:13Z", "lastUpdate": "2025-08-31T22:25:13.264963Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaSBT", "description": "MetaSBT is a scalable framework designed to automatically index microbial genomes and accurately characterize metagenome-assembled genomes using Sequence Bloom Trees.", "homepage": "https://github.com/cumbof/MetaSBT", "biotoolsID": "metasbt", "biotoolsCURIE": "biotools:metasbt", "version": [ "0.1.4.post1", "0.1.5" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cumbof/MetaSBT", "type": [ "Repository" ], "note": "Framework Repository" }, { "url": "https://github.com/cumbof/MetaSBT-DBs", "type": [ "Repository" ], "note": "Repository with Public MetaSBT Databases" } ], "download": [ { "url": "https://pypi.io/packages/source/m/metasbt/metasbt-0.1.4.post1.tar.gz", "type": "Software package", "note": null, "version": "0.1.4" } ], "documentation": [ { "url": "https://github.com/cumbof/MetaSBT/wiki", "type": [ "General" ], "note": "Official MetaSBT Wiki" } ], "publication": [], "credit": [ { "name": "Fabio Cumbo", "email": "fabio.cumbo@gmail.com", "url": "https://cumbof.github.io", "orcidid": "https://orcid.org/0000-0003-2920-5838", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null } ], "owner": "fabiocumbo", "additionDate": "2025-06-17T20:53:54.551980Z", "lastUpdate": "2025-08-29T00:30:28.809173Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProteinProspector", "description": "A suite of protein identification tools.", "homepage": "http://prospector.ucsf.edu", "biotoolsID": "proteinprospector", "biotoolsCURIE": "biotools:proteinprospector", "version": [], "otherID": [ { "value": "RRID:SCR_014558", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3647", "term": "Blind peptide database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3489", "term": "Database management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://prospector.ucsf.edu/prospector/html/instruct/allman.htm", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1074/mcp.d500002-mcp200", "pmid": "15937296", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cells, time-of-flight mass spectrometer: II New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets", "abstract": "A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR instrument. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine \"Mascot\" using a new results comparison program within Prospector named \"SearchCompare.\" The results from this study demonstrate that the high quality data produced on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.", "date": "2005-08-01T00:00:00Z", "citationCount": 165, "authors": [ { "name": "Chalkley R.J." }, { "name": "Baker P.R." }, { "name": "Huang L." }, { "name": "Hansen K.C." }, { "name": "Allen N.P." }, { "name": "Rexach M." }, { "name": "Burlingame A.L." } ], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [ { "name": "Admin", "email": "ppadmin@cgl.ucsf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:18Z", "lastUpdate": "2025-08-28T15:15:11.245617Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "VAPOR", "description": "VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.", "homepage": "https://github.com/wm75/vaporup", "biotoolsID": "vapor", "biotoolsCURIE": "biotools:vapor", "version": [ "1.0.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/connor-lab/vapor", "type": [ "Other" ], "note": "Original VAPOR repository from which versions prior to 1.0.3 were released" } ], "download": [ { "url": "https://pypi.org/project/vaporup/#files", "type": "Software package", "note": null, "version": null }, { "url": "https://doi.org/10.5281/zenodo.15364147", "type": "Biological data", "note": "A curated collection of reference sequences for each influenza A genome segment that can be used with the tool for classification of sequences from this virus", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btz814", "pmid": "31693070", "pmcid": "PMC7703727", "type": [], "version": null, "note": null, "metadata": { "title": "Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications", "abstract": "Motivation: Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results: Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of > 99:8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses.", "date": "2020-01-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Southgate J.A." }, { "name": "Bull M.J." }, { "name": "Brown C.M." }, { "name": "Watkins J." }, { "name": "Corden S." }, { "name": "Southgate B." }, { "name": "Moore C." }, { "name": "Connor T.R." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "Kigaard", "additionDate": "2020-01-14T09:34:01Z", "lastUpdate": "2025-08-28T14:32:58.093703Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "wm75" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Make2D-DB II", "description": "Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web.", "homepage": "https://world-2dpage.expasy.org/make2ddb/", "biotoolsID": "make2d-db_ii", "biotoolsCURIE": "biotools:make2d-db_ii", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://world-2dpage.expasy.org/make2ddb/1.Readme_main.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.200300483", "pmid": "12923769", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Make 2D-DB II package: Conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases", "abstract": "The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.", "date": "2003-08-01T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Mostaguir K." }, { "name": "Hoogland C." }, { "name": "Binz P.-A." }, { "name": "Appel R.D." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:40Z", "lastUpdate": "2025-08-28T13:43:51.088758Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Swiss Mass Abacus", "description": "Calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.", "homepage": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "biotoolsID": "swiss_mass_abacus", "biotoolsCURIE": "biotools:swiss_mass_abacus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0122", "term": "Structural genomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:54Z", "lastUpdate": "2025-08-28T13:43:28.119620Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Glydin", "description": "Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures.", "homepage": "https://glycoproteome.expasy.org/epitopes/", "biotoolsID": "glydin", "biotoolsCURIE": "biotools:glydin", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/epitopes/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:30Z", "lastUpdate": "2025-08-28T13:41:40.603256Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IScan", "description": "A package to identify insertion sequences and similar transposable elements, their inverted repeats, and the direct target repeats they generate in entire genomes.", "homepage": "https://www.expasy.org/resources/iscan", "biotoolsID": "iscan", "biotoolsCURIE": "biotools:iscan", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ieu.uzh.ch/wagner/software/IScan/index.html", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:10Z", "lastUpdate": "2025-08-28T13:33:36.585259Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ASAP", "description": "ASAP (Assemble Species by Automatic Partitioning) is a method to build species partitions from single locus sequence alignments.\nASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity.", "homepage": "https://bioinfo.mnhn.fr/abi/public/asap", "biotoolsID": "asap-assemble", "biotoolsCURIE": "biotools:asap-assemble", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3478", "term": "Phylogenetic reconstruction" }, { "uri": "http://edamontology.org/operation_3200", "term": "DNA barcoding" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://bioinfo.mnhn.fr/abi/public/asap/help_asap.html", "type": [ "General" ], "note": null }, { "url": "https://bioinfo.mnhn.fr/abi/public/asap/FAQ_asap.html", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1111/1755-0998.13281", "pmid": "33058550", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ASAP: assemble species by automatic partitioning", "abstract": "© 2020 John Wiley & Sons LtdHere, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.", "date": "2021-02-01T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Puillandre N." }, { "name": "Brouillet S." }, { "name": "Achaz G." } ], "journal": "Molecular Ecology Resources" } } ], "credit": [ { "name": "Nicolas Puillandre", "email": "puillandre@mnhn.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Kigaard", "additionDate": "2021-01-18T11:19:37Z", "lastUpdate": "2025-08-28T07:33:58.127682Z", "editPermission": { "type": "group", "authors": [ "arkamukherjee" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ArrayAnalysis", "description": "ArrayAnalysis is a web-based application for transcriptomic data analysis. It supports the analysis of both microarray and RNA-seq data. The tool may also be installed locally as a desktop app, Docker image, or R package.", "homepage": "https://www.arrayanalysis.org", "biotoolsID": "arrayanalysis.org", "biotoolsCURIE": "biotools:arrayanalysis.org", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "CC-BY-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.arrayanalysis.org", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkt293", "pmid": "23620278", "pmcid": "PMC3692049", "type": [], "version": null, "note": null, "metadata": { "title": "User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.", "abstract": "Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large amounts of data are produced with complex technologies. For DNA microarrays, specific algorithms for QC and pre-processing including normalization have been developed by the scientific community, especially for expression chips of the Affymetrix platform. Many of these have been implemented in the statistical scripting language R and are available from the Bioconductor repository. However, application is hampered by lack of integrative tools that can be used by users of any experience level. To fill this gap, we developed a freely available tool for QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org or downloaded for local use in R. The portal provides extensive documentation, including user guides, interpretation help with real output illustrations and detailed technical documentation. It assists newcomers to the field in performing state-of-the-art QC and pre-processing while offering data analysts an integral open-source package. Providing the scientific community with this easily accessible tool will allow improving data quality and reuse and adoption of standards.", "date": "2013-01-01T00:00:00Z", "citationCount": 107, "authors": [ { "name": "Eijssen L.M." }, { "name": "Jaillard M." }, { "name": "Adriaens M.E." }, { "name": "Gaj S." }, { "name": "de Groot P.J." }, { "name": "Muller M." }, { "name": "Evelo C.T." } ], "journal": "Nucleic acids research" } }, { "doi": "10.1186/s12864-015-1689-8", "pmid": "26122086", "pmcid": "PMC4486126", "type": [], "version": null, "note": null, "metadata": { "title": "A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal", "abstract": "Background: Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. Results: To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. Conclusions: The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org. A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.", "date": "2015-06-30T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Eijssen L.M.T." }, { "name": "Goelela V.S." }, { "name": "Kelder T." }, { "name": "Adriaens M.E." }, { "name": "Evelo C.T." }, { "name": "Radonjic M." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Support Forum", "email": null, "url": "https://www.arrayanalysis.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jarnokoetsier", "additionDate": "2017-05-16T12:28:07Z", "lastUpdate": "2025-08-28T07:09:05.106319Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UCPH COVID19 DASHBOARD", "description": "The dashboard provides tools for visualizing the COVID-19 spread in individual countries over time, as well as comparing different countries on a similar time scale. 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Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.", "date": "2021-01-01T00:00:00Z", "citationCount": 32, "authors": [ { "name": "Lee J." }, { "name": "Shah M." }, { "name": "Ballouz S." }, { "name": "Crow M." }, { "name": "Gillis J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jesse Gillis", "email": "jgillis@cshl.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Kigaard", "additionDate": "2021-01-18T08:31:27Z", "lastUpdate": "2025-08-27T10:44:27.458203Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "datmat", "description": "‘datmat’ is a Python package aimed to easily gather data from a variety of sources and materialize it into a standardized format. 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