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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FRETBursts Resource Report Resource Website 1+ mentions |
FRETBursts (RRID:SCR_016898) | FRETBursts | data analysis software, data processing software, software application, software resource, 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 GM069709; NIGMS R01 GM95904 |
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 | 2026-09-19 12:53:30 | 3 | ||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | data analysis software, data processing software, image analysis software, software application, software resource | 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 | 2026-09-19 12:53:30 | 18 | ||||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | data analysis software, data processing software, software application, software resource | 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 |
NIDA P30 DA018310; NIGMS R01 GM067193 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-09-19 12:53:30 | 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 | data or information resource, organization portal, portal, service resource, training resource | 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 | 2026-09-19 12:53:30 | 0 | ||||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | analysis service resource, data analysis service, data or information resource, database, production service resource, 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 |
Baylor College of Medicine Medical Scientist Training Program ; Belfer Foundation ; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; NCI P30 CA06516; NCRR R24 RR032668; NHGRI U01 HG007709; NIGMS R01 GM067761; NIGMS R01 GM067858; NIGMS R01 GM084947; NIGMS R01 GM120033; NIH Office of the Director R24 OD021997; NIH Office of the Director R24 OD022005; NINDS 1U54NS093793; NINDS U54 NS093793; NSF DMS 1263932; Simons Foundation ; T T Chao Family Foundation ; The Robert and Janice McNair Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-09-19 12:53:29 | 25 | ||||
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PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | data analysis software, data processing software, network analysis software, software application, software resource | 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 |
Bergen Research Foundation ; European Research Council ; NHGRI U41 HG003751; NIGMS U54 GM114833; Research Council of Norway |
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 | 2026-09-19 12:53:29 | 1 | ||||||
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Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | data processing software, data visualization software, software application, software resource | 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 | Alfred P. Sloan research fellowship ; NCI R01 CA157304; NCI U01 CA184897; NHGRI R01 HG002439; NIGMS R01 GM085319; NIGMS R01 GM096193; NSF IIS 1149662; Starr Cancer Consortium |
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 | 2026-09-19 12:53:29 | 0 | |||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data analysis software, data processing software, software application, software resource | 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 | Carver Chair in Molecular Medicine ; Fraternal Order of Eagles Diabetes Research Center ; NHLBI R24 HL123482; NIDDK R01 DK115791; NIDDK R24 DK096518; NIGMS T32 GM082729; University of Iowa Center for Gene Therapy |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-09-19 12:53:32 | 5 | |||||||||
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Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data analysis software, data processing software, software application, software resource | 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 |
NCRR P20 RR016460; NIGMS P20 GM103429; NSFC 61272016; NSFC 61432010 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-09-19 12:53:33 | 6 | ||||||
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nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | JDRF ; NCI R33 CA225248; NIBIB R21 EB020976; NIDDK DP3 DK110844; NIDDK UC4 DK104167; NIGMS P41 GM103493; NIH Office Of The Director S10 OD016350 |
PMID:29491378 | SCR_017129 | 2026-09-19 12:53:34 | 1 | |||||||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data access protocol, data or information resource, data repository, service resource, software resource, storage service resource, web service | 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 |
NHGRI U54 HG008097; NIGMS R01 GM103551; NIGMS R01 GM121696; 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 | 2026-09-19 12:53:34 | 0 | ||||||
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CWL-Airflow Resource Report Resource Website 1+ mentions |
CWL-Airflow (RRID:SCR_017196) | CWL DAG | data processing software, software application, software resource, workflow software | Software Python package to extend Airflow functionality with Common Workflow Language support. Lightweight pipeline manager supporting Common Workflow Language. Can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on cloud platforms. | airflow, common workflow language, cwl, pipeline, workflow, docker | is listed by: OMICtools | NCATS UL1 TR001425; NIGMS DP2 GM119134 |
DOI:10.1101/249243 DOI:10.1093/gigascience/giz084 |
Free, Available for download, Freely available | OMICS_26560 | SCR_017196 | CWL-Airflow v 1.0.16, Common Workflow Language-Airflow | 2026-09-19 12:53:36 | 3 | |||||
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FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 | Lawrence Berkeley National Lab IDAT program ; NCRR U54 RR022220; NIGMS P41 GM109824; NIGMS R01 GM083960; NIGMS R01 GM105404; Rinat (Pfizer) Inc. ; Weizmann Institute Advancing Women in Science |
PMID:23972848 PMID:27151198 |
Free, Available for download, Freely available | SCR_017269 | Fast X-Ray Scattering | 2026-09-19 12:53:37 | 24 | |||||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | 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 |
NHGRI HG005998; NIGMS P50 GM071508; NIGMS R01 GM071966 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-09-19 12:53:39 | 8 | ||||||||
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microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | data processing software, image analysis software, image processing software, software application, software resource | 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 |
National Science Foundation Graduate Research Fellowship Program ; NIDA DA018310; NIGMS T32 GM070421; NIMH U01 MH109062; Springborn Fellowship |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-09-19 12:53:40 | 1 | |||||||
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BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | data analysis software, data processing software, sequence analysis software, software application, software resource, 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 |
EMBL ; European Research Council ; Max Planck Society ; NIGMS U01 GM110749; Royal Society of New Zealand Marsden award ; Swiss National Science foundation |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-09-19 12:53:38 | 211 | |||||||
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Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, 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 |
NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-09-19 12:53:43 | 6 | ||||||
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BindingDB Resource Report Resource Website 10+ mentions |
BindingDB (RRID:SCR_000390) | data or information resource, database | Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs . | drug, drug discovery, drug target, binding affinity, protein interaction, small molecule-protein interaction, interaction, protein, small molecule, FASEB list |
is related to: PSICQUIC Registry is related to: canSAR has parent organization: University of California at San Diego; California; USA |
National Institute of Standards and Technology ; NIGMS GM070064; NIGMS R24 GM144232; NSF 9808318 |
PMID:26481362 PMID:17145705 |
Free, Freely available | r3d100012074, nif-0000-02603 | https://doi.org/10.17616/R3ZS9T | SCR_000390 | BindingDB | 2026-09-19 12:56:26 | 41 | |||||
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Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, software resource, source code | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-09-19 12:56:29 | 0 | |||||||
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WTCHG Genome Scan Viewer Resource Report Resource Website 1+ mentions |
WTCHG Genome Scan Viewer (RRID:SCR_001635) | GSCANDB | data or information resource, database, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements. | genome, gene, snp, trait, genotype, phenotype, visualization, region, chromosome, quantitative trait locus, hybridization, gene expression | has parent organization: University of Oxford; Oxford; United Kingdom | NIAAA U01AA014425; NCRR R24RR015116; NIGMS R01GM072863; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153902 | SCR_001635 | Wellcome Trust Centre for Human Genetics Genome Scan Viewer, Genome Scan Viewer, Genome Scan Database | 2026-09-19 12:56:31 | 3 |
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