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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | software application, data analysis software, software resource, data processing software, network analysis software | Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. | mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools |
is listed by: Galaxy is listed by: OMICtools is listed by: Debian is listed by: bio.tools works with: Reactome |
European Research Council ; Research Council of Norway ; Bergen Research Foundation ; NIGMS U54 GM114833; NHGRI U41 HG003751 |
DOI:10.1101/375097 | Free, Available for download, Freely available | BioTools:PathwayMatcher, biotools:PathwayMatcher | https://anaconda.org/bioconda/pathwaymatcher, https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher | SCR_016759 | 2026-07-28 09:44:26 | 1 | ||||||
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Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | software application, service resource, data or information resource, data repository, data processing software, software resource, image acquisition software, storage service resource, portal, data acquisition software | System designed for automated collection of images from a transmission electron microscope. | automated, collection, acquisition, data, image, electron, microscope |
uses: Python Programming Language has parent organization: Scripps Research Institute |
NCRR RR17573; NIGMS GM61939; NSF DBI0352386; NSF DBI9730056; NSF DBI9904547 |
PMID:15890530 | Free, Available for download, Freely available, Registration suggested | SCR_016731 | 2026-07-28 09:44:22 | 42 | ||||||||
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PMI-Byonic Resource Report Resource Website 10+ mentions |
PMI-Byonic (RRID:SCR_016735) | Byonic | software application, software resource, data analysis software, data processing software | Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type. | Byonic, Protein Metrics Inc., peptide, protein, identification, mass, spectrometry | NIGMS R21 GM085718 | PMID:23255153 | Commercially available | SCR_016735 | Protein Metrics Inc. Byonic, PMI-Byonic, PMI Byonic, Byonic | 2026-07-28 09:44:22 | 22 | |||||||
|
PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | software application, software resource, data analysis software, data processing software | Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype. | detect, gene, disease, associate, trait, mechanism, molecular, variation, phenotype | NCI K12 CA139160; NCI F32CA165823; NIMH T32 MH020065; NIMH R01 MH101820; NIMH R01 MH090937; NIGMS U01 GM61393; NIMH P50 MH094267; NIGMS U01 GM092691; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | 2026-07-28 09:44:22 | 23 | |||||||||
|
FRETBursts Resource Report Resource Website 1+ mentions |
FRETBursts (RRID:SCR_016898) | FRETBursts | software application, data analysis software, software resource, data processing software, software toolkit | Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data. | freely, diffusing, single, molecule, FRET, smFRET, cellular, process, intermolecular, interaction, conformational, change, biomacromolecule, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM95904; NIGMS R01 GM069709 |
PMID:27532626 | Free, Available for download, Freely available | biotools:fretbursts | https://opensmfs.github.io/FRETBursts/, https://bio.tools/fretbursts | SCR_016898 | Förster Resonance Energy Transfer Bursts, FRETBursts | 2026-07-28 09:44:29 | 2 | ||||
|
CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | software application, data analysis software, software resource, data processing software, image analysis software | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-07-28 09:44:25 | 17 | ||||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | software application, software resource, data analysis software, data processing software | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIGMS R01 GM067193; NIDA P30 DA018310 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-07-28 09:44:26 | 14 | ||||||
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National Resource for Translational and Developmental Proteomics Resource Report Resource Website |
National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) | NRTDP | service resource, training resource, data or information resource, organization portal, portal | Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists. | protein, mass, spectrometry, proteomics, measurement, targeted, untargeted, analysis |
has parent organization: Northwestern University; Illinois; USA provides: ProSight Lite |
NIGMS P41 GM108569 | SCR_016907 | The National Resource for Translational and Developmental Proteomics, NRTDP | 2026-07-28 09:44:29 | 0 | ||||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-07-28 09:44:25 | 22 | ||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | software application, software resource, data analysis software, data processing software | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | NIDDK R24 DK096518; NHLBI R24 HL123482; NIDDK R01 DK115791; Fraternal Order of Eagles Diabetes Research Center ; University of Iowa Center for Gene Therapy ; Carver Chair in Molecular Medicine ; NIGMS T32 GM082729 |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-07-28 09:44:27 | 5 | |||||||||
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Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | data visualization software, software resource, software application, data processing software | Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. | quantitative, visualization, aligned, RNA-Seq, read, data, compare, exon, usage, sample, experiment, condition, MISO | is related to: MISO | NCI R01 CA157304; Starr Cancer Consortium ; NIGMS R01 GM096193; NSF IIS 1149662; Alfred P. Sloan research fellowship ; NIGMS R01 GM085319; NCI U01 CA184897; NHGRI R01 HG002439 |
PMID:25617416 DOI:10.1093/bioinformatics/btv034 |
Free, Available for download, Freely available | http://miso.readthedocs.org/en/fastmiso/sashimi.html | SCR_016861 | sashimi_plot | 2026-07-28 09:44:25 | 0 | |||||
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Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | software application, software resource, data analysis software, data processing software | Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcripto, assembler, RNAseq, data, short, read, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NSFC 61432010; NSFC 61272016; NCRR P20 RR016460; NIGMS P20 GM103429 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-07-28 09:44:28 | 6 | ||||||
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | service resource, data or information resource, data repository, data access protocol, software resource, web service, storage service resource | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NIGMS R01 GM103551; NIGMS R01 GM121696; NHGRI U54 HG008097; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-07-28 09:44:27 | 0 | ||||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-07-28 09:44:29 | 7 | ||||||||
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FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data. | computing, theoretical, scattering, profile, structure, fitting, small, angle, X ray, data | has parent organization: University of California at San Francisco; California; USA | Weizmann Institute Advancing Women in Science ; NIGMS R01 GM083960; NCRR U54 RR022220; NIGMS R01 GM105404; Rinat (Pfizer) Inc. ; Lawrence Berkeley National Lab IDAT program ; NIGMS P41 GM109824 |
PMID:23972848 PMID:27151198 |
Free, Available for download, Freely available | SCR_017269 | Fast X-Ray Scattering | 2026-07-28 09:44:28 | 20 | |||||||
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BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
Royal Society of New Zealand Marsden award ; European Research Council ; NIGMS U01 GM110749; Swiss National Science foundation ; Max Planck Society ; EMBL |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-07-28 09:44:33 | 194 | |||||||
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Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | software resource, data access protocol, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-07-28 09:44:38 | 4 | ||||||
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microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | software application, software resource, data processing software, image processing software, image analysis software | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | Image, guided, mass, spectrometry, automatic, cell, finding, point, based, registration, whole, slide, image, analysis, processing, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIDA DA018310; NIMH U01 MH109062; National Science Foundation Graduate Research Fellowship Program ; Springborn Fellowship ; NIGMS T32 GM070421 |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-07-28 09:44:35 | 1 | |||||||
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Polbase Resource Report Resource Website |
Polbase (RRID:SCR_006107) | service resource, data or information resource, data repository, database, storage service resource | Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software. | dna polymerase repository, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PubMed is related to: UniProt has parent organization: New England Biolabs |
Small Business Innovation Research ; NIGMS 1R44GM087021 |
PMID:21993301 | Free, Open unspecified license, Acknowledgement required | biotools:polbase, nlx_151580 | https://bio.tools/polbase | SCR_006107 | DNA Polymerase Database | 2026-07-28 09:41:27 | 0 | |||||
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QTL Archive Resource Report Resource Website 1+ mentions |
QTL Archive (RRID:SCR_006213) | QTL Archive | service resource, data set, data or information resource, data repository, storage service resource | Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive. | quantitative trait locus, inbred rat strain, phenotype, cross, genetics, inbreeding, genetic marker, quantitative genetics |
is listed by: re3data.org has parent organization: Jackson Laboratory |
NIGMS R01 GM070683 | The community can contribute to this resource | r3d100010571, nlx_151757 | https://doi.org/10.17616/R3C02Z | http://qtlarchive.org/ | SCR_006213 | Quantitative Trait Loci (QTL) Archive, Quantitative Trait Loci Archive | 2026-07-28 09:41:33 | 6 |
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