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compounds in a single sample, but unreliable feature extraction and metabolite identification remain considerable barriers to their interpretation and usefulness. peakPantheR (Peak Picking and ANnoTation of High-resolution Experiments in R) is an R package for the targeted extraction and integration of annotated features from LC-MS profiling experiments. 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Since the last major update in 2015, MetaboAnalyst has continued to evolve based on user feedback and technological advancements in the field. For this year's update, four newkey features have been added to MetaboAnalyst 4.0, including: (1) real-time R command tracking and display coupled with the release of a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for prediction of pathway activity from untargeted mass spectral data using themummichog algorithm; (3) a Biomarker Metaanalysis module for robust biomarker identification through the combination of multiple metabolomic datasets and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. The user interface of MetaboAnalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions. The underlying knowledgebases (compound libraries, metabolite sets, and metabolic pathways) have also been updated based on the latest data from the Human Metabolome Database (HMDB). A Docker image of MetaboAnalyst is also available to facilitate download and local installation of Metabo-Analyst.", "date": "2018-07-02T00:00:00Z", "citationCount": 2833, "authors": [ { "name": "Chong J." }, { "name": "Soufan O." }, { "name": "Li C." }, { "name": "Caraus I." }, { "name": "Li S." }, { "name": "Bourque G." }, { "name": "Wishart D.S." }, { "name": "Xia J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1038/s41596-022-00710-w", "pmid": "35715522", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data", "abstract": "Liquid chromatography coupled with high-resolution mass spectrometry (LC–HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the well-established MetaboAnalyst platform (www.metaboanalyst.ca) This protocol extends the previous 2011 Nature Protocol by providing stepwise instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC–HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata. Parameter optimization may take ~2 h to complete depending on the server load, and the remaining three stages may be executed in ~60 min.", "date": "2022-08-01T00:00:00Z", "citationCount": 730, "authors": [ { "name": "Pang Z." }, { "name": "Zhou G." }, { "name": "Ewald J." }, { "name": "Chang L." }, { "name": "Hacariz O." }, { "name": "Basu N." }, { "name": "Xia J." } ], "journal": "Nature Protocols" } } ], "credit": [ { "name": null, "email": "jeff.xia@mcgill.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-07-03T00:07:39Z", "lastUpdate": "2025-11-03T16:45:45.351615Z", "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": "IsoCor", "description": "IsoCor is a scientific software dedicated to the correction of low- and high-resolution mass spectrometry (MS) data for naturally occuring isotopes. IsoCor corrects raw MS data (mass fractions) for naturally-occurring isotopes of all elements and purity of the isotopic tracer. The output of IsoCor is the isotopologue distribution of the molecule (i.e. the relative fractions of molecular entities differing only in the number of isotopic substitutions of the tracer). IsoCor also calculates the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.", "homepage": "https://github.com/MetaSys-LISBP/IsoCor", "biotoolsID": "IsoCor", "biotoolsCURIE": "biotools:IsoCor", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Library", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3955", "term": "Fluxomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Compute" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/MetaSys-LISBP/IsoCor", "type": [ "Repository" ], "note": "GitHub repository" }, { "url": "https://isocor.readthedocs.io/en/latest/", "type": [ "Helpdesk" ], "note": "Documentation" }, { "url": "https://toolshed.g2.bx.psu.edu/view/gmat/isocor/96f7617b4848", "type": [ "Galaxy service" ], "note": "Galaxy tool shed" }, { "url": "https://pypi.org/project/IsoCor/", "type": [ "Repository" ], "note": "PyPi repository" }, { "url": "https://anaconda.org/bioconda/isocor", "type": [ "Repository" ], "note": "Bioconda repository" } ], "download": [ { "url": "https://github.com/MetaSys-LISBP/IsoCor", "type": "Source code", "note": null, "version": "2" } ], "documentation": [ { "url": "https://isocor.readthedocs.io/en/latest/", "type": [ "API documentation", "Command-line options", "FAQ", "Installation instructions", "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btz209", "pmid": "30903185", "pmcid": null, "type": [ "Method" ], "version": "2", "note": null, "metadata": { "title": "IsoCor: Isotope correction for high-resolution MS labeling experiments", "abstract": "© 2019 The Author(s) 2019. Published by Oxford University Press. All rights reserved.Summary: Mass spectrometry (MS) is widely used for isotopic studies of metabolism and other (bio)chemical processes. Quantitative applications in systems and synthetic biology require to correct the raw MS data for the contribution of naturally occurring isotopes. Several tools are available to correct low-resolution MS data, and recent developments made substantial improvements by introducing resolution-dependent correction methods, hence opening the way to the correction of high-resolution MS (HRMS) data. Nevertheless, current HRMS correction methods partly fail to determine which isotopic species are resolved from the tracer isotopologues and should thus be corrected. We present an updated version of our isotope correction software (IsoCor) with a novel correction algorithm which ensures to accurately exploit any chemical species with any isotopic tracer, at any MS resolution. IsoCor v2 also includes a novel graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines. Availability and implementation: IsoCor v2 is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/IsoCor/ and https://isocor.readthedocs.io/.", "date": "2019-11-01T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Millard P." }, { "name": "Delepine B." }, { "name": "Guionnet M." }, { "name": "Heuillet M." }, { "name": "Bellvert F." }, { "name": "Letisse F." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Pierre Millard", "email": "millard@insa-toulouse.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-8136-9963", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Matthieu Guionnet", "email": "guionnet@insa-toulouse.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-5326-0357", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Baudoin Delépine", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-6288-425X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "millard", "additionDate": "2020-01-21T09:25:21Z", "lastUpdate": "2025-11-03T16:16:25.029297Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TEtranscripts", "description": "TEtranscripts is a software package for including transposable elements in differential expression analysis of RNA-seq datasets. It assigns reads to genes and transposable elements, performs differential expression testing, and provides statistical analysis for transposable element expression.", "homepage": "https://hammelllab.labsites.cshl.edu/software/#TEtranscripts", "biotoolsID": "tetranscripts", "biotoolsCURIE": "biotools:tetranscripts", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Gene expression data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "TEtranscripts --mode TE --input <input_file> --output <output_file>" } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/mhammell-laboratory/TEtranscripts", "type": [ "Repository" ], "note": null }, { "url": "https://www.mghlab.org/software/tetranscripts", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/mhammell-laboratory/TEtranscripts", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/mhammell-laboratory/TEtranscripts", "type": [ "Installation instructions", "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv422", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets", "abstract": "", "date": "2015-05-25T00:00:00Z", "citationCount": 419, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Molly Gale Hammell", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0405-8392", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "samuelruizperez", "additionDate": "2025-10-27T16:45:48.395441Z", "lastUpdate": "2025-10-27T16:50:09.756484Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SHAMAN", "description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].", "homepage": "http://shaman.c3bi.pasteur.fr/", "biotoolsID": "shaman", "biotoolsCURIE": "biotools:shaman", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" }, { "uri": "http://edamontology.org/operation_3221", "term": "Species frequency estimation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": "Quantitative metagenomics Count table & taxonomy Diversity, barplot, boxplot, scatterplot, rarefaction curves, heatmap", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/aghozlane/shaman", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://shaman.c3bi.pasteur.fr/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1073/pnas.1523899113", "pmid": "27140611", "pmcid": "PMC4878514", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection", "abstract": "Listeria monocytogenes is responsible for gastroenteritis in healthy individuals and for a severe invasive disease in immunocompromised patients. Among the three identified L. monocytogenes evolutionary lineages, lineage I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms underlying the higher virulence potential of strains of this lineage remain elusive. Here, we demonstrate that Listeriolysin S (LLS), a virulence factor only present in a subset of lineage I strains, is a bacteriocin highly expressed in the intestine of orally infected mice that alters the host intestinal microbiota and promotes intestinal colonization by L. monocytogenes, as well as deeper organ infection. To our knowledge, these results therefore identify LLS as the first bacteriocin described in L. monocytogenes and associate modulation of host microbiota by L. monocytogenes epidemic strains to increased virulence.", "date": "2016-05-17T00:00:00Z", "citationCount": 87, "authors": [ { "name": "Quereda J.J." }, { "name": "Dussurget O." }, { "name": "Nahori M.-A." }, { "name": "Ghozlane A." }, { "name": "Volant S." }, { "name": "Dillies M.-A." }, { "name": "Regnault B." }, { "name": "Kennedy S." }, { "name": "Mondot S." }, { "name": "Villoing B." }, { "name": "Cossart P." }, { "name": "Pizarro-Cerda J." } ], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } } ], "credit": [ { "name": "Stevenn Volant", "email": null, "url": "https://research.pasteur.fr/en/member/stevenn-volant/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Hugo Varet", "email": null, "url": "https://research.pasteur.fr/en/member/hugo-varet/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pierre Lechat", "email": null, "url": "https://research.pasteur.fr/en/member/pierre-lechat/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Amine Ghozlane", "email": null, "url": "https://research.pasteur.fr/en/member/amine-ghozlane/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Institut Pasteur", "email": null, "url": "https://research.pasteur.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "C3BI", "email": null, "url": "https://research.pasteur.fr/en/center/c3bi/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics Hub", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "SHAMAN team", "email": "shaman@pasteur.fr", "url": "https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aghozlane", "additionDate": "2016-11-28T10:07:16Z", "lastUpdate": "2025-10-23T10:46:59.953305Z", "editPermission": { "type": "group", "authors": [ "hmenager", "khillion", "vashokan" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Dynamont", "description": "A Dynamic Programming Approach to Segment ONT Signals. 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The workflow is designed to comprehensively detect all variant types (SNV. MNV, InDel, SV, CNV, Fusions, Viral insertions, Telomere length, Genetic Immune Escape, mutational processes) as well as key tumor characteristics (purity, ploidy, TMB, MSI) from data derived from different short read platforms. The tooling is optimised for paired whole genome samples (90x tumor, 30x normal) but can be run on exome or panel (targeted) data. There is support for GRCh37 and GRCh38 human reference genome builds.", "homepage": "https://github.com/nf-core/oncoanalyser/tree/dev", "biotoolsID": "oncoanalyser", "biotoolsCURIE": "biotools:oncoanalyser", "version": [ "5.34" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/nf-core/oncoanalyser/tree/dev", "type": [ "Issue tracker", "Repository" ], "note": "GitHub page for issue tracking of Nextflow workflow implementation" }, { "url": "https://github.com/hartwigmedical/hmftools", "type": [ "Repository", "Issue tracker" ], "note": "GitHub repository of underlying tools with issue tracking" } ], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "jdeligt", "additionDate": "2024-03-07T20:51:08.529472Z", "lastUpdate": "2025-10-09T07:39:49.943872Z", "editPermission": { "type": "group", "authors": [ "jdeligt", "VKasalica" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "NApy", "description": "An efficient Python tool providing statistical tests for large-scale heterogeneous data with enhanced support for missing data", "homepage": "https://github.com/DyHealthNet/NApy", "biotoolsID": "napy", "biotoolsCURIE": "biotools:napy", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3658", "term": "Statistical inference" } ], "input": [ { "data": { "uri": 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"2025-09-25T09:40:57.232559Z", "lastUpdate": "2025-09-25T09:48:41.530316Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Constava", "description": "Constava calculates conformational states probability and conformational state variability from protein structure ensembles.", "homepage": "https://pypi.org/project/constava/", "biotoolsID": "constava", "biotoolsCURIE": "biotools:constava", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0249", "term": "Protein geometry calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2991", "term": "Protein geometry data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2016", "term": "Amino acid property" }, "format": [] } ], "note": "This command analyzes the provided backbone dihedral angles and infers the propensities for each residue to reside in a given conformational state.", "cmd": "constava analyze" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bio2byte/constava", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/Bio2Byte/constava/releases/tag/v1.1.0", "type": "Source code", "note": "Source code in tar.gz or zip formats.", "version": "1.1.0" } ], "documentation": [ { "url": "https://pypi.org/project/constava/", "type": [ "Command-line options" ], "note": "Table of content: \nDescription\nInstallation\nPrerequisites\nInstallation through PyPI\nInstallation from the source\nUsage\nExecution from the command line\nExtracting backbone dihedrals from a trajectory\nAnalyzing a conformational ensemble\nGenerating custom conformational state models\nExecution as a python library\nExtracting backbone dihedrals as a DataFrame\nSetting parameters and analyzing a conformational ensemble\nGenerating and loading conformational state models\nConstava-class parameters vs. command line arguments\nLicense\nAuthors\nAcknowledgements\nContact" } ], "publication": [ { "doi": "10.1093/nargab/lqae082", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Data-driven probabilistic definition of the low energy conformational states of protein residues", "abstract": "", "date": "2024-09-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "NAR Genomics and Bioinformatics" } }, { "doi": "10.1016/j.jmb.2024.168900", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics", "abstract": "", "date": "2025-01-15T00:00:00Z", "citationCount": 3, "authors": [], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Wim Vranken", "email": "wim.vranken@vub.be", "url": "https://bio2byte.be/people/31", "orcidid": "https://orcid.org/0000-0001-7470-4324", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "W.V., D.R. and G.O. conceptualised the study. W.V., D.R., G.O. and D.B. provided supervision. W.V. provided the NMR data and directed the project." }, { "name": "José Gavalda-Garcia", "email": null, "url": "https://bio2byte.be/people/38", "orcidid": "https://orcid.org/0000-0001-6431-3442", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "J.G.-G. and D.B. developed, implemented and validated the method." }, { "name": "David Bickel", "email": null, "url": "https://bio2byte.be/people/47", "orcidid": "https://orcid.org/0000-0003-0332-8338", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "W.V., D.R., G.O. and D.B. provided supervision. J.G.-G. and D.B. developed, implemented and validated the method." }, { "name": "Adrián Díaz", "email": "adrian.diaz@vub.be", "url": "https://bio2byte.be/people/48", "orcidid": "https://orcid.org/0000-0003-0165-1318", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": "A.D. contributed in the distribution of this software." }, { "name": "Daniele Raimondi", "email": null, "url": "https://orcid.org/0000-0003-1157-1899", "orcidid": "https://orcid.org/0000-0003-1157-1899", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "W.V., D.R. and G.O. conceptualised the study. W.V., D.R., G.O. and D.B. provided supervision." }, { "name": "Gabriele Orlando", "email": null, "url": "https://orcid.org/0000-0002-5935-5258", "orcidid": "https://orcid.org/0000-0002-5935-5258", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "W.V., D.R. and G.O. conceptualised the study. G.O. developed the initial methodology. W.V., D.R., G.O. and D.B. provided supervision." }, { "name": "Bio2Byte", "email": "bio2byte@vub.be", "url": "https://bio2byte.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Joel Roca-Martinez", "email": null, "url": "https://orcid.org/0000-0002-4313-3845", "orcidid": "https://orcid.org/0000-0002-4313-3845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "J.R.-M. performed the MD simulations." } ], "owner": "adrian.diaz", "additionDate": "2025-09-23T08:54:29.614497Z", "lastUpdate": "2025-09-23T08:54:29.626822Z", "editPermission": { "type": "group", "authors": [ "wvranken@vub.ac.be", "adrian.diaz" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "methylR", "description": "Graphical interface for comprehensive DNA methylation array data analysis.", "homepage": "https://methylr.research.liu.se", "biotoolsID": "methylr", "biotoolsCURIE": "biotools:methylr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3204", "term": "Methylation analysis" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_3928", "term": "Pathway analysis" }, { "uri": "http://edamontology.org/operation_2939", "term": "Principal component visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3110", "term": "Raw microarray data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0916", "term": "Gene report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3754", "term": "GO-term enrichment data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3953", "term": "Pathway overrepresentation data" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" }, { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "JavaScript", "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/JD2112/methylr", "type": [ "Repository" ], "note": null }, { "url": "https://groups.google.com/g/methylr", "type": [ "Discussion forum" ], "note": null }, { "url": "https://sourceforge.net/projects/methylr/", "type": [ "Repository" ], "note": null }, { "url": "http://methylr.netlify.app", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/r/jd21/methylr", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://methylr.netlify.app/methylysis", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btad184", "pmid": "37039839", "pmcid": "PMC10125902", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "methylR: a graphical interface for comprehensive DNA methylation array data analysis", "abstract": "Motivation: DNA methylation analysis using arrays is a widely used method in research and clinical studies to study Epigenetics. Although several packages have been published to incur the results, most of them require a deep computational knowledge to perform the analysis. To resolve the limitation and to offer an easily accessible solution for researchers, we developed methylR a graphical tool that can analyze not only the raw data but also performs different downstream analyses with a few mouse clicks. Results: We used standard and established open-source published packages or pipelines in methylR. We evaluated a publicly available dataset and compared the published results with those obtained with our tool. We implemented eight downstream analysis modules that can perform multidimensional analyses to pathway enrichment. Although the main application is designed for Illumina DNA methylation array data analysis, we made the accessory modules suitable for other kinds of data analysis as well. Availability and implementation: Freely available at Github: https://github.com/JD2112/methylr; Webserver: https://methylr.research.liu.se.", "date": "2023-04-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Volpe M." }, { "name": "Das J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Jyotirmoy Das", "email": "jyotirmoy.das@liu.se", "url": null, "orcidid": "https://orcid.org/0000-0002-5649-4658", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "jd21", "additionDate": "2023-09-15T19:04:20.592395Z", "lastUpdate": "2025-09-22T16:50:36.936901Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TwistMethylFlow", "description": "This Nextflow pipeline is designed for the analysis of Twist NGS Methylation data, including quality control, alignment, methylation calling, differential methylation analysis, and post-processing. 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"typeEntity": null, "typeRole": [], "note": null }, { "name": "Tian Hong", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-8212-7050", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "haimei", "additionDate": "2025-08-20T17:28:51.309591Z", "lastUpdate": "2025-08-20T18:13:15.065957Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MacSyLib", "description": "a Python package library that allow to model and detect macromolecular systems, genetic pathways… by similarity search in prokaryotes datasets.", "homepage": "https://github.com/gem-pasteur/macsylib", "biotoolsID": "macsylib", "biotoolsCURIE": "biotools:macsylib", "version": [ "1.0.1" ], "otherID": [], "relation": [ { "biotoolsID": "macsyfinder", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": 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"Other" ], "note": null }, { "url": "https://macsylib.readthedocs.io/en/latest/", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://github.com/gem-pasteur/macsylib", "type": "Source code", "note": null, "version": "1.0.1" }, { "url": "https://pypi.org/project/MacSyLib/", "type": "Software package", "note": null, "version": "1.0.1" } ], "documentation": [ { "url": "https://macsylib.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.24072/pcjournal.250", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes", "abstract": "Complex cellular functions are usually encoded by a set of genes in one or a few orga-nized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models’ constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular mod-els: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder.", "date": "2023-01-01T00:00:00Z", "citationCount": 43, "authors": [ { "name": "Neron B." }, { "name": "Denise R." }, { "name": "Coluzzi C." }, { "name": "Touchon M." }, { "name": "Rocha E.P.C." }, { "name": "Abby S.S." } ], "journal": "Peer Community Journal" } } ], "credit": [ { "name": "Institut Pasteur", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "0495fxg12", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Microbial Evolutionary Genomics Unit", "email": null, "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics HUB", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Eduardo P.C. Rocha", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7704-822X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sophie Abby", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5231-3346", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bertrand Néron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0220-0482", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bneron", "additionDate": "2025-08-07T10:25:22.118390Z", "lastUpdate": "2025-08-11T12:14:42.322020Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EukCC", "description": "EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.", "homepage": "https://github.com/EBI-Metagenomics/EukCC", "biotoolsID": "eukcc", "biotoolsCURIE": "biotools:eukcc", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13059-020-02155-4", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC", "abstract": "Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.", "date": "2020-09-10T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Saary P." }, { "name": "Mitchell A.L." }, { "name": "Finn R.D." } ], "journal": "Genome Biology" } } ], "credit": [], "owner": "m.bernt", "additionDate": "2025-07-24T07:14:51.692628Z", "lastUpdate": "2025-07-24T07:14:51.694965Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ETENLNC", "description": "ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and analysis framework", "homepage": "https://github.com/EvolOMICS-TU/ETENLNC", "biotoolsID": "etenlnc", "biotoolsCURIE": "biotools:etenlnc", "version": [ "1.0" 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"format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_0906", "term": "Protein interaction data" }, "format": [] } ], "note": "Run ETENLNC on paired-end raw RNA-Seq (.fastq) data", "cmd": "bash ETENLNC_docker.sh" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/EvolOMICS-TU/ETENLNC", "type": [ "Repository" ], "note": "GitHub Repo" } ], "download": [ { "url": 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A detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication).", "version": "1.0" } ], "documentation": [ { "url": "https://github.com/EvolOMICS-TU/ETENLNC", "type": [ "Command-line options" ], "note": "A detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication)" } ], "publication": [ { "doi": "10.1016/j.compbiolchem.2024.108140", "pmid": "38996755", "pmcid": null, "type": [ "Primary" ], "version": ".0", "note": null, "metadata": { "title": "ETENLNC: An end to end lncRNA identification and analysis framework to facilitate construction of known and novel lncRNA regulatory networks", "abstract": "Long non-coding RNAs (lncRNAs) play crucial roles in the regulation of gene expression and maintenance of genomic integrity through various interactions with DNA, RNA, and proteins. The availability of large-scale sequence data from various high-throughput platforms has opened possibilities to identify, predict, and functionally annotate lncRNAs. As a result, there is a growing demand for an integrative computational framework capable of identifying known lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding), a user-friendly, integrative, open-source, scalable, and modular computational framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC employs six stringent filtration steps to identify novel lncRNAs, performs differential expression analysis of mRNA and lncRNA transcripts, and predicts regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked ETENLNC against six existing tools and optimized it for desktop workstations and high-performance computing environments using data from three different species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.", "date": "2024-10-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Nath P." }, { "name": "Bhuyan K." }, { "name": "Bhattacharyya D.K." }, { "name": "Barah P." } ], "journal": "Computational Biology and Chemistry" } } ], "credit": [ { "name": "Pankaj Barah", "email": "barah@tezu.ernet.in", "url": "https://www.tezu.ernet.in/dmbbt/profile/34", "orcidid": "https://orcid.org/0000-0001-7039-7996", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer" ], "note": "Assistant Professor at Department of Molecular Biology and Biotechnology, Tezpur University." }, { "name": "Prangan Nath", "email": "prangannathofficial@gmai.com", "url": null, "orcidid": "https://orcid.org/0000-0002-9451-7822", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "prangannath", "additionDate": "2025-07-23T10:27:57.572501Z", "lastUpdate": "2025-07-23T10:27:57.574879Z", "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": "SQANTI3", "description": "SQANTI3 constitutes the first module of the Functional IsoTranscriptomics (FIT) pipeline, which is an end-to-end strategy to perform isoform-level bioinformatics analyses. \n\nThe SQANTI3 tool is designed to enable quality control and filtering of long read-defined transcriptomes, which are often rich in artifacts and false-positive isoforms. \n\nTherefore, a good curation of the transcriptome is indispensable to proceed with FIT analysis and produce valid, biologically sound conclusions/hypothesis.", "homepage": "https://github.com/ConesaLab/SQANTI3", "biotoolsID": "sqanti3", "biotoolsCURIE": "biotools:sqanti3", "version": [ "5.5" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/ConesaLab/SQANTI3", "type": [ "Repository" ], "note": "Github repository for source code access and download" } ], "download": [ { "url": "https://github.com/ConesaLab/SQANTI3/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://github.com/ConesaLab/SQANTI3/releases/download/v5.5/SQANTI3_v5.5.zip", "type": "Binaries", "note": "Version 5.5 download link from github", "version": "5.5" } ], "documentation": [ { "url": "https://github.com/ConesaLab/SQANTI3/wiki", "type": [ "General" ], "note": "SQANTI3 main documentation resource" }, { "url": "https://github.com/ConesaLab/SQANTI3/blob/master/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-Quality-Control", "type": [ "Command-line options" ], "note": "Command-line options and instructions for the QC submodule" }, { "url": "https://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-filter", "type": [ "Command-line options" ], "note": "Command-line options and instructions for the filter submodule" }, { "url": "https://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-rescue", "type": [ "Command-line options" ], "note": "Command-line options and instructions for the rescue submodule" }, { "url": "https://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installation", "type": [ "Installation instructions" ], "note": "Instructions to install and use sqanti, either in docker or apptainer containers or in a linux system" }, { "url": "https://github.com/ConesaLab/SQANTI3/wiki/Tutorial:-running-SQANTI3-on-an-example-dataset", "type": [ "Quick start guide" ], "note": "Basic tutorial with examples to start using SQANTI3" }, { "url": "https://github.com/ConesaLab/SQANTI3/releases", "type": [ "Release notes" ], "note": "Changelog and release notes for every version" }, { "url": "https://github.com/ConesaLab/SQANTI3?tab=readme-ov-file#how-to-cite-sqanti3", "type": [ "Citation instructions" ], "note": "Citation instructions are on the end of the Github repository's main page" }, { "url": "https://github.com/ConesaLab/SQANTI3/wiki/SQANTI3-memory-requeriments-and-paralellization", "type": [ "Other" ], "note": "Benchmarking about the resources needed to run sqanti3 with multiple cores" } ], "publication": [ { "doi": "10.1038/s41592-024-02229-2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "5.1", "note": "Publication of SQANTI3", "metadata": { "title": "SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms", "abstract": "SQANTI3 offers a flexible tool for quality control, curation and annotation of long-read RNA sequencing data. SQANTI3 is a tool designed for the quality control, curation and annotation of long-read transcript models obtained with third-generation sequencing technologies. Leveraging its annotation framework, SQANTI3 calculates quality descriptors of transcript models, junctions and transcript ends. With this information, potential artifacts can be identified and replaced with reliable sequences. Furthermore, the integrated functional annotation feature enables subsequent functional iso-transcriptomics analyses.", "date": "2024-05-01T00:00:00Z", "citationCount": 41, "authors": [ { "name": "Pardo-Palacios F.J." }, { "name": "Arzalluz-Luque A." }, { "name": "Kondratova L." }, { "name": "Salguero P." }, { "name": "Mestre-Tomas J." }, { "name": "Amorin R." }, { "name": "Estevan-Morio E." }, { "name": "Liu T." }, { "name": "Nanni A." }, { "name": "McIntyre L." }, { "name": "Tseng E." }, { "name": "Conesa A." } ], "journal": "Nature Methods" } }, { "doi": "10.1101/gr.222976.117", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": "Original SQANTI publication", "metadata": { "title": "SQANTI: Extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification", "abstract": "High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read-based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases, we find that alternative isoforms are elusive to proteogenomics detection. SQANTI allows the user to maximize the analytical outcome of long-read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes.", "date": "2018-03-01T00:00:00Z", "citationCount": 256, "authors": [ { "name": "Tardaguila M." }, { "name": "De La Fuente L." }, { "name": "Marti C." }, { "name": "Pereira C." }, { "name": "Pardo-Palacios F.J." }, { "name": "Del Risco H." }, { "name": "Ferrell M." }, { "name": "Mellado M." }, { "name": "Macchietto M." }, { "name": "Verheggen K." }, { "name": "Edelmann M." }, { "name": "Ezkurdia I." }, { "name": "Vazquez J." }, { "name": "Tress M." }, { "name": "Mortazavi A." }, { "name": "Martens L." }, { "name": "Rodriguez-Navarro S." }, { "name": "Moreno-Manzano V." }, { "name": "Conesa A." } ], "journal": "Genome Research" } } ], "credit": [ { "name": "Ana Conesa", "email": "ana.conesa@csic.es", "url": null, "orcidid": "https://orcid.org/0000-0001-9597-311X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Pablo Atienza", "email": "pablo.atienza@csic.es", "url": null, "orcidid": "https://orcid.org/0009-0002-1093-693X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": "Maintainer of SQANTI3" }, { "name": "Fabián Robledo", "email": "fabian.robledo@csic.es", "url": null, "orcidid": "https://orcid.org/0009-0005-9047-3315", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": "Maintainer of SQANTI3 and ELIXIR-related contact" } ], "owner": "Fabian-RY", "additionDate": "2025-07-07T09:04:03.787249Z", "lastUpdate": "2025-07-07T09:35:33.280160Z", "editPermission": { "type": "group", "authors": [ "Fabian-RY" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "16SMicrobiomeMLFS", "description": "Code and supporting data for the article: \"Exploring the role of normalization and feature selection in microbiome disease classification pipelines.\"", "homepage": "https://github.com/nach00gar/16SMicrobiomeMLFS", "biotoolsID": "16smicrobiomemlfs", "biotoolsCURIE": "biotools:16smicrobiomemlfs", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/nach00gar/16SMicrobiomeMLFS", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Ignacio Garach Vélez", "email": "igarachv@ugr.es", "url": "https://github.com/nach00gar/16SMicrobiomeMLFS", "orcidid": "https://orcid.org/0009-0006-6618-7949", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "igarachv", "additionDate": "2025-07-04T16:10:32.821423Z", "lastUpdate": "2025-07-04T16:10:32.823947Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DeepSig", "description": "Prediction of secretory signal peptides in protein sequences", "homepage": "https://busca.biocomp.unibo.it/deepsig/", "biotoolsID": "deepsig", "biotoolsCURIE": "biotools:deepsig", "version": [ "1.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0418", "term": "Protein signal peptide detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "C++" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": "Source code", "note": null, "version": "1.2.5" }, { "url": "https://hub.docker.com/r/bolognabiocomp/deepsig", "type": "Container file", "note": null, "version": "1.2.5" } ], "documentation": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx818", "pmid": "29280997", "pmcid": "PMC5946842", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "DeepSig: Deep learning improves signal peptide detection in proteins", "abstract": "Motivation The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website.", "date": "2018-05-15T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": "http://biocomp.unibo.it", "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2018-05-28T14:50:09Z", "lastUpdate": "2025-06-19T11:55:09.017105Z", "editPermission": { "type": "group", "authors": [ "savo", "ELIXIR-ITA-BOLOGNA" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "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 }, { "name": "quickmerge", "description": "Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.", "homepage": "https://github.com/mahulchak/quickmerge", "biotoolsID": "quickmerge", "biotoolsCURIE": "biotools:quickmerge", "version": [ "v.0.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [ { "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": "Runs whole merge process on an input assembly.\nAssembly 2 will be used to fill gaps in assembly 1.", "cmd": "merge_wrapper.py -pre output_prefix assembly_1.fa assembly_2.fa" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "C++", "C" ], "license": "GPL-3.0", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/mahulchak/quickmerge/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/mahulchak/quickmerge", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1534/g3.118.200162", "pmid": "30018084", "pmcid": "PMC6169397", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Rapid low-cost assembly of the drosophila melanogaster reference genome using low-coverage, long-read sequencing", "abstract": "Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from largescale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using highcoverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).", "date": "2018-10-01T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Solares E.A." }, { "name": "Chakraborty M." }, { "name": "Miller D.E." }, { "name": "Kalsow S." }, { "name": "Hall K." }, { "name": "Perera A.G." }, { "name": "Emerson J.J." }, { "name": "Scott Hawley R." } ], "journal": "G3: Genes, Genomes, Genetics" } } ], "credit": [ { "name": "Mahul Chakraborty", "email": null, "url": "https://mahulchakraborty.wordpress.com/", "orcidid": "https://orcid.org/0000-0003-2414-9187", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-27T09:04:45Z", "lastUpdate": "2025-06-18T12:17:20.983962Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "Keiler_Collier" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pavian", "description": "Web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in metagenomics classification results is often complicated by host and laboratory contaminants as well as many non-pathogenic microbiota. Researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams.", "homepage": "https://ccb.jhu.edu/software/pavian/", "biotoolsID": "pavian", "biotoolsCURIE": "biotools:pavian", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Animal and Crop Genomics", "Biodiversity", "microbiome" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/fbreitwieser/pavian/tree/master", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://ccb.jhu.edu/software/pavian/index.shtml?t=manual", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/084715", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": null, "email": "fbreitw1@jhmi.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-08-20T16:34:27Z", "lastUpdate": "2025-06-17T15:12:54.095225Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "wtv", "description": "A CLI/python library that selects characteristic qualitative ions based on \nhttps://github.com/yuanhonglun/WTV_2.0", "homepage": "https://recetox.github.io/wtv/", "biotoolsID": "wtv", "biotoolsCURIE": "biotools:wtv", "version": [ "0.0.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3936", "term": "Feature selection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_4039", "term": "MSP" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_4039", "term": "MSP" } ] } ], "note": null, "cmd": "wtv-cli --msp_path input.msp --outpath output --mz_min 35 --mz_max 400 ..." } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": null, "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://github.com/RECETOX/wtv", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/RECETOX/wtv", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/wtv/", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/RECETOX/galaxytools/tree/master/tools/wtv", "type": "Tool wrapper (Galaxy)", "note": null, "version": null } ], "documentation": [ { "url": "https://recetox.github.io/wtv/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.molp.2024.04.012", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "WTV2.0: A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode", "abstract": "Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles. However, the annotation coverage achieved using current untargeted and widely targeted volatomics (WTV) methods has been limited by low sensitivity and/or low acquisition coverage. Here, we introduce WTV 2.0, which enabled the construction of a high-coverage library containing 2111 plant volatiles, and report the development of a comprehensive selective ion monitoring (cSIM) acquisition method, including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method, that can acquire the smallest but sufficient number of ions for most plant volatiles, as well as the automatic qualitative and semi-quantitative analysis of cSIM data. Importantly, the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library, utilizing the obtained cSIM data. We showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method, doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit, and led to the discovery of menthofuran as a novel flavor compound in passion fruit. WTV 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.", "date": "2024-06-03T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Yuan H." }, { "name": "Jiangfang Y." }, { "name": "Liu Z." }, { "name": "Su R." }, { "name": "Li Q." }, { "name": "Fang C." }, { "name": "Huang S." }, { "name": "Liu X." }, { "name": "Fernie A.R." }, { "name": "Luo J." } ], "journal": "Molecular Plant" } } ], "credit": [], "owner": "acquayefrank", "additionDate": "2025-06-02T12:24:30.535794Z", "lastUpdate": "2025-06-12T09:26:29.793603Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bracken", "description": "Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample).", "homepage": "https://ccb.jhu.edu/software/bracken/", "biotoolsID": "bracken", "biotoolsCURIE": "biotools:bracken", "version": [], "otherID": [], "relation": [ { "biotoolsID": "kraken2", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" } ], "operatingSystem": [ "Linux" ], "language": [ "Perl", "Python" ], "license": "GPL-3.0", "collectionID": [ "Animal and Crop Genomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/jenniferlu717/Bracken", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/jenniferlu717/Bracken/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://ccb.jhu.edu/software/bracken/index.shtml?t=manual", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj-cs.104", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Bracken: Estimating species abundance in metagenomics data", "abstract": "Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomalRNAgene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.", "date": "2017-01-01T00:00:00Z", "citationCount": 1084, "authors": [ { "name": "Lu J." }, { "name": "Breitwieser F.P." }, { "name": "Thielen P." }, { "name": "Salzberg S.L." } ], "journal": "PeerJ Computer Science" } } ], "credit": [ { "name": null, "email": "jlu26@jhmi.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-08-20T15:17:20Z", "lastUpdate": "2025-06-11T12:25:29.118910Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "ELIXIR-CZ", "bebatut", "vashokan" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
