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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | workflow software, software resource, software application, data processing software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NIGMS R01 GM126019; NHLBI U54 HL127624; NHGRI U24HG012674; NIAID R03AI159286 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-08-03 09:37:03 | 1 | ||||||||
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | software resource, data processing software, software application, data analysis software | Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. | High density genotyping data, molecular phenotype, gene expression, proteomics, mapping trait loci, diversity outbred mice, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM074244; NIGMS R01 GM070683; NIGMS R01 GM123489 |
PMID:30591514 | Free, Available for download, Freely available | biotools:R_qtl2, SCR_020965 | https://bio.tools/R_qtl2, https://kbroman.org/qtl2, https://github.com/rqtl/qtl2 | SCR_018181 | QTL, R/quantitative trait loci, QTL2, Quantitative Trait Locus 2, quantitative trait loci 2, R/qtl, qtl2 | 2026-08-03 09:37:13 | 13 | |||||
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ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | web service, data access protocol, service resource, software resource | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R35 GM118078; NIGMS R01 GM061867 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-08-03 09:37:13 | 858 | |||||||
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CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | sequence analysis software, software toolkit, software application, data processing software, data analysis software, software resource | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI RM1 HG009490; NIBIB R01 EB022376; NIGMS R35 GM118062; NIGMS R35 GM118158; NIDDK R03 DK109232; NHLBI P01 HL32262; NHGRI R00 HG008399; NIDDK P30 DK049216; NHLBI R01 HL119099; NHGRI R01 HG005085 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2, https://github.com/pinellolab/CRISPResso | SCR_021538 | CRISPResso2 | 2026-08-03 09:37:24 | 21 | |||||||
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RepEnrich Resource Report Resource Website 10+ mentions |
RepEnrich (RRID:SCR_021733) | software resource, data processing software, software application, data analysis software | Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data. | profile enrichment, next generation sequencing reads, transposable elements, estimate repetitive element enrichment, genome wide transcriptional regulation, sequencing data | has parent organization: Brown University; Rhode Island; USA | NIA K25 AG028753; NIGMS T32 GM007601; NIA R37 AG016694 |
PMID:25012247 | Free, Available for download, Freely available | https://github.com/nerettilab/RepEnrich2 | SCR_021733 | RepEnrich2 | 2026-08-03 09:37:37 | 21 | ||||||
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DeepCell Resource Report Resource Website 10+ mentions |
DeepCell (RRID:SCR_022197) | software application, data processing software, segmentation software, image analysis software, software resource | Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software. | segmenting individual cells, microscopy image, cell segmentation | Paul Allen Family Foundation ; NIGMS F32 GM119319; NIGMS P50 GM107615; NLM DP1 LM01150 |
DOI:10.1371/journal.pcbi.1005177 | Free, Available for download, Freely available | SCR_022197 | Deepcell | 2026-08-03 09:37:49 | 10 | ||||||||
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Simbios Resource Report Resource Website 1+ mentions |
Simbios (RRID:SCR_004320) | organization portal, portal, postdoctoral program resource, journal article, data or information resource, software resource, training resource | Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers. |
is related to: Biomedical Computation Review is related to: National Centers for Biomedical Computing has parent organization: Stanford University; Stanford; California is parent organization of: Simtk.org is parent organization of: Biomedical Computation Review is parent organization of: BioSimulation Course |
NIGMS U54 GM072970 | PMID:22081222 PMID:20107615 |
nlx_33018 | SCR_004320 | Simbios - NIH Center for Biomedical Computation at Stanford, physics-based Simulation of Biological Structures | 2026-08-03 09:32:39 | 1 | ||||||||
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SCIRun Resource Report Resource Website 10+ mentions |
SCIRun (RRID:SCR_002541) | SCIRun | software toolkit, software application, data processing software, simulation software, software resource, data visualization software | A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6. | modeling, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BioMesh3D is related to: BioMesh3D is related to: BioPSE is related to: BioPSE has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Free, Available for download, Freely available | nlx_155949 | http://www.nitrc.org/projects/scirun | SCR_002541 | 2026-08-03 09:31:53 | 21 | ||||||
|
ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | image processing software, software toolkit, software application, data processing software, image analysis software, software resource | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NINDS ; NIGMS RC2 GM092519; Wellcome Trust Strategic Award 095931; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; NIH ; NIMH |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, nif-0000-30467, SCR_018407 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-08-03 09:32:11 | 27070 | ||||
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FRETBursts Resource Report Resource Website 1+ mentions |
FRETBursts (RRID:SCR_016898) | FRETBursts | software toolkit, software application, data processing software, data analysis software, software resource | 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 | 2026-08-03 09:36:38 | 2 | ||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | software application, data processing software, data analysis software, image analysis software, 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 | 2026-08-03 09:36:28 | 17 | ||||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | software resource, data processing software, software application, data analysis 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 | 2026-08-03 09:36:28 | 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 | organization portal, portal, service resource, data or information 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 | 2026-08-03 09:36:38 | 0 | ||||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | production service resource, data analysis service, data or information resource, database, analysis 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 |
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 | 2026-08-03 09:36:37 | 22 | ||||
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PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | network analysis software, software application, data processing software, data analysis software, 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 |
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 | 2026-08-03 09:36:57 | 1 | ||||||
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Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | data repository, portal, image acquisition software, data acquisition software, software application, service resource, data processing software, storage service resource, data or information resource, software resource | 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 | 2026-08-03 09:36:26 | 42 | ||||||||
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PMI-Byonic Resource Report Resource Website 10+ mentions |
PMI-Byonic (RRID:SCR_016735) | Byonic | software resource, data processing software, software application, data analysis 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 | 2026-08-03 09:36:57 | 22 | |||||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | software resource, data processing software, software application, data analysis 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 | 2026-08-03 09:36:35 | 23 | |||||||||
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Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | software resource, data visualization software, 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 | 2026-08-03 09:36:27 | 0 | |||||
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data repository, web service, data or information resource, storage service resource, data access protocol, service resource, software 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 | 2026-08-03 09:36:32 | 0 |
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