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{ "count": 9131, "next": "?page=2", "previous": null, "list": [ { "name": "REFUTE", "description": "REFUTE is an open benchmark for scientific critique honesty and epistemic calibration on recent life-science and biomedical literature. It tests whether models keep claims inside what the evidence allows (overclaim / planted-flaw / falsifier selection) and whether stated confidence is calibrated, with judge-free MCQ axes plus open-ended critique scoring.", "homepage": "https://bgpt.pro/refute", "biotoolsID": "bgpt-refute", "biotoolsCURIE": "biotools:bgpt-refute", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/connerlambden/refute-inspect", "type": [ "Repository" ], "note": null }, { "url": "https://huggingface.co/datasets/BGPT-OFFICIAL/refute", "type": [ "Other" ], "note": "Hugging Face dataset" }, { "url": "https://doi.org/10.5281/zenodo.21542238", "type": [ "Other" ], "note": "Zenodo preprint DOI" }, { "url": "https://www.openml.org/d/47266", "type": [ "Other" ], "note": "OpenML REFUTE-knowledge-v3" }, { "url": "https://www.openml.org/d/47268", "type": [ "Other" ], "note": "OpenML REFUTE-soundness-v3" }, { "url": "https://doi.org/10.7910/DVN/IGAJWO", "type": [ "Other" ], "note": "Harvard Dataverse dataset" }, { "url": "https://ascl.net/code/v/4795", "type": [ "Other" ], "note": "ASCL software entry" }, { "url": "https://www.wikidata.org/wiki/Q140690703", "type": [ "Other" ], "note": "Wikidata item" }, { "url": "https://osf.io/qxyfe/", "type": [ "Other" ], "note": "OSF project" }, { "url": "https://www.saashub.com/refute", "type": [ "Other" ], "note": "SaaSHub listing" } ], "download": [], "documentation": [ { "url": "https://bgpt.pro/refute", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.5281/zenodo.21542238", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Interim preprint deposit on Zenodo (v3.0.0-preprint).", "metadata": null } ], "credit": [ { "name": "Conner Lambden", "email": "contact@bgpt.pro", "url": "https://bgpt.pro", "orcidid": "https://orcid.org/0000-0003-0162-6622", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bgpt_pro", "additionDate": "2026-07-24T23:18:01.380915Z", "lastUpdate": "2026-07-25T00:53:14.294442Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CBRA", "description": "Workflow optimized for the analysis of rare diseases, designed to detect SNVs, INDELs , CNVs and SVs in targeted sequencing data (CES/WES) and whole genome sequencing (WGS), built on Nextflow and following nf-core standards. It has an advanced variant annotation optimized for rare diseases diagnosis and discovery.", "homepage": "https://github.com/CIBERER/CBRA", "biotoolsID": "nf-cbra-snvs", "biotoolsCURIE": "biotools:nf-cbra-snvs", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "MIT", "collectionID": [ "IMPaCT-ISCIII", "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CIBERER/CBRA", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/CIBERER/CBRA", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "pminguez", "additionDate": "2025-08-12T09:03:01.228796Z", "lastUpdate": "2026-07-23T13:38:22.115020Z", "editPermission": { "type": "group", "authors": [ "yolandabq", "cristina.a.s" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Rosin-Rammler Diagram plotting tool", "description": "This tool plots the Rosin-Rammler Diagram (RRSB) and calculates various related parameters.", "homepage": "https://www.mathworks.com/matlabcentral/fileexchange/28013-rosin-rammler-diagram-plotting-tool", "biotoolsID": "rrsb-plot", "biotoolsCURIE": "biotools:rrsb-plot", "version": [ "1.16.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "MATLAB" ], "license": null, "collectionID": [ "MATLAB", "File Exchange" ], "maturity": null, "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://www.mathworks.com//matlabcentral/mlc-downloads/downloads/submissions/28013/versions/17/screenshot.png", "type": "Screenshot", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [ { "name": "Ivan Brezani", "email": null, "url": "https://www.mathworks.com/matlabcentral/profile/2241235-ivan-brezani", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "zsmag19", "additionDate": "2021-05-05T11:09:42Z", "lastUpdate": "2026-07-21T21:16:00.781732Z", "editPermission": { "type": "group", "authors": [ "Verena_H" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pangolin", "description": "Pangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences.", "homepage": "https://github.com/tkzeng/Pangolin", "biotoolsID": "pangolin", "biotoolsCURIE": "biotools:pangolin", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0433", "term": "Splice site prediction" }, { "uri": "http://edamontology.org/operation_0232", "term": "Sequence merging" }, { "uri": "http://edamontology.org/operation_0264", "term": "Alternative splicing prediction" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3320", "term": "RNA splicing" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_3676", "term": "Exome sequencing" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13059-022-02664-4", "pmid": "35449021", "pmcid": "PMC9022248", "type": [], "version": null, "note": null, "metadata": { "title": "Predicting RNA splicing from DNA sequence using Pangolin", "abstract": "Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pangolin outperforms state-of-the-art methods for predicting RNA splicing on a variety of prediction tasks. Pangolin improves prediction of the impact of genetic variants on RNA splicing, including common, rare, and lineage-specific genetic variation. In addition, Pangolin identifies loss-of-function mutations with high accuracy and recall, particularly for mutations that are not missense or nonsense, demonstrating remarkable potential for identifying pathogenic variants.", "date": "2022-12-01T00:00:00Z", "citationCount": 52, "authors": [ { "name": "Zeng T." }, { "name": "Li Y.I." } ], "journal": "Genome Biology" } } ], "credit": [ { "name": "Yang I Li", "email": "yangili1@uchicago.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-0736-251X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Tony Zeng", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-07-26T10:11:09.660345Z", "lastUpdate": "2026-07-21T21:15:53.848510Z", "editPermission": { "type": "group", "authors": [ "xiangjun_zhao" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ArrayAnalysis", "description": "ArrayAnalysis is a web-based application for transcriptomic data analysis. It supports the analysis of both microarray and RNA-seq data. The tool may also be installed locally as a desktop app, Docker image, or R package.", "homepage": "https://www.arrayanalysis.org", "biotoolsID": "arrayanalysis.org", "biotoolsCURIE": "biotools:arrayanalysis.org", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "CC-BY-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.arrayanalysis.org", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkt293", "pmid": "23620278", "pmcid": "PMC3692049", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1186/s12864-015-1689-8", "pmid": "26122086", "pmcid": "PMC4486126", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.64898/2026.07.13.738193", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Jarno Koetsier", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7981-1345", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Lars Eijssen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6473-2839", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "jarnokoetsier", "additionDate": "2017-05-16T12:28:07Z", "lastUpdate": "2026-07-21T13:11:30.168837Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PinPath", "description": "PinPath enables flexible visualization of (omics) data onto pathways diagrams, allowing users to pinpoint where the relevant changes occur. It supports pathway diagrams from WikiPathways and KEGG, as well as custom GPML and KGML files. Data can be displayed on both native pathway layouts and network representations", "homepage": "https://synum-lab.github.io/PinPath-web/", "biotoolsID": "pinpath", "biotoolsCURIE": "biotools:pinpath", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [], "language": [ "R" ], "license": "MIT", "collectionID": [ "Bioconductor" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/SyNUM-lab/PinPath", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://synum-lab.github.io/PinPath-web/", "type": [ "General" ], "note": null }, { "url": "https://doi.org/doi:10.18129/B9.bioc.PinPath", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Jarno Koetsier", "email": "jarno.koetsier@maastrichtuniversity.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-7981-1345", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Lars Eijssen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6473-2839", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Egon Willighagen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7542-0286", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "jarnokoetsier", "additionDate": "2026-07-21T12:43:59.527995Z", "lastUpdate": "2026-07-21T13:08:40.683127Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "picklet", "description": "Browser-based tool to open almost any sequence file — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, SCF, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PIR and more — see every sequence inside, pick the ones you want, and save them as FASTA. The format is detected from the file content, not from the extension, so unlabelled or misnamed files still open. Runs entirely in the browser — files are never uploaded.", "homepage": "https://fishka.bio/picklet", "biotoolsID": "picklet", "biotoolsCURIE": "biotools:picklet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2121", "term": "Sequence file editing" }, { "uri": "http://edamontology.org/operation_0233", "term": "Sequence conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1632", "term": "SCF" }, { "uri": "http://edamontology.org/format_3000", "term": "AB1" }, { "uri": "http://edamontology.org/format_1963", "term": "UniProtKB format" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "TypeScript" ], "license": "Freeware", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://fishka.bio", "type": [ "Software catalogue" ], "note": "fishka.bio — the tool collection picklet belongs to" } ], "download": [ { "url": "https://fishka.bio/download", "type": "Downloads page", "note": "Offline build — the same application as a self-contained archive, runs from local files with no server", "version": null } ], "documentation": [], "publication": [ { "doi": "10.5281/zenodo.21444547", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "2026.07.19", "note": "Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including picklet.", "metadata": null } ], "credit": [ { "name": "Fishka Bio", "email": "swim@fishka.bio", "url": "https://fishka.bio", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null } ], "owner": "fishka", "additionDate": "2026-07-11T21:51:46.808639Z", "lastUpdate": "2026-07-20T00:49:56.618062Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ab1lens", "description": "Browser-based viewer for Sanger sequencing chromatograms in AB1/ABIF and SCF format. Opens .ab1/.abi/.fsa files, shows raw and analysed traces, basecalls, quality values and the ABIF directory, and puts two reads side by side for comparison. Aligns a read against a reference sequence to highlight mismatches. Exports the read as FASTA, FASTQ or ABIF and the chromatogram as a high-resolution image. 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