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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Drug Target Ontology Resource Report Resource Website 1+ mentions |
Drug Target Ontology (RRID:SCR_015581) | DTO | controlled vocabulary, data or information resource, ontology | Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. | drug ontology, drug target ontology, protein family | has parent organization: University of Miami; Florida; USA | NCI U54CA189205; NHLBI U54HL127624 |
Available for download | https://github.com/DrugTargetOntology/DTO http://bioportal.bioontology.org/ontologies/DTO | SCR_015581 | SciCrunch Registry | Drug Target Ontology (DTO) | 2026-10-17 01:29:12 | 2 | ||||||
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GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | data analysis software, data processing software, software application, software resource | Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme. | GEO2Enrichr, gene expression signatures, enrichment analyses, multiple studies, biological theme, bio.tools |
is listed by: bio.tools is listed by: Debian works with: Gene Expression Omnibus (GEO) |
NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27846806 | Free, Freely available | biotools:gen3va | https://github.com/MaayanLab/gen3va, https://bio.tools/gen3va | SCR_015682 | SciCrunch Registry | GENE Expression and Enrichment Vector Analyzer | 2026-10-17 01:29:14 | 5 | |||||
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CRowd Extracted Expression of Differential Signatures Resource Report Resource Website 1+ mentions |
CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) | CREEDS | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures. | variant, disease expression, disease marker | NIGMS R01GM098316; NHLBI U54HL127624; NCI U54CA189201 |
PMID:27667448 | Freely available, Free, Available for download | SCR_015680 | SciCrunch Registry | CREEDS: CRowd Extracted Expression of Differential Signatures | 2026-10-17 01:29:02 | 6 | |||||||
|
Rosetta Resource Report Resource Website 100+ mentions |
Rosetta (RRID:SCR_015701) | simulation software, software application, software resource, software toolkit | Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Molecular modeling, structure prediction, computational modeling, protein analysis, enzyme design, macromolecular complexes |
is used by: trRosetta is related to: PyRosetta works with: ROSIE |
Hertz Foundation Fellowship ; NCI F32 CA189246; NIGMS GM078221; NIGMS GM084453; NIGMS GM092802; NIGMS GM110089; NIGMS GM111819; NIGMS GM114961; NIGMS GM117189; NIGMS GM73141; NSF Graduate Research Fellowship ; NSF BMAT 1507736; Simons Foundation |
PMID:28430426 PMID:21829626 PMID:18442991 |
Restricted | SCR_015701 | SciCrunch Registry | Rosetta modeling software | 2026-10-17 01:29:00 | 216 | |||||||
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VaDiR Resource Report Resource Website 10+ mentions |
VaDiR (RRID:SCR_015797) | VaDiR | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets. | rna-seq, somatic variant calling, ovarian cancer, cancer genomes transcriptome, orthogonal validation, genetic mutation, sequence variation analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Biostatistics and Informatics Shared Resource (BISR) ; Cancer Center Cancer Biology program ; Department of Defense Ovarian Cancer Research Program W81XWH-10-1-0386; NCI P30 CA168524; University of Kansas Endowment Association |
DOI:10.5524/100360 | Free, Available for download | biotools:vadir | ftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/, https://bio.tools/vadir | SCR_015797 | SciCrunch Registry | VaDiR: an integrated approach to Variant Detection in RNA | 2026-10-17 01:28:57 | 14 | ||||
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L1000 Characteristic Direction Signature Search Engine Resource Report Resource Website 1+ mentions |
L1000 Characteristic Direction Signature Search Engine (RRID:SCR_016177) | L1000CDS2 | data access protocol, data or information resource, data set, database, service resource, software resource, web service | LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction. | signature, gene, dataset, ligand, characteristic, expression, benchmark |
is related to: LINCS Joint Project - Breast Cancer Network Browser has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U54 CA189201; NHLBI U54 HL127624 |
PMID:28413689 | Free, Freely available | SCR_016177 | SciCrunch Registry | 2026-10-17 01:29:22 | 8 | |||||||
|
Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | SciCrunch Registry | 2026-10-17 01:29:04 | 142 | |||||||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | data analysis software, data processing software, software application, software resource | 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 F32CA165823; NCI K12 CA139160; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595; NIGMS U01 GM092691; NIGMS U01 GM61393; NIMH P50 MH094267; NIMH R01 MH090937; NIMH R01 MH101820; NIMH T32 MH020065 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | SciCrunch Registry | 2026-10-17 01:29:32 | 25 | |||||||||
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ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | data analysis software, data processing software, software application, software resource | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; NCI U24 CA126554; Thomas G. Labrecque Foundation |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | SciCrunch Registry | 2026-10-17 01:29:20 | 196 | ||||||
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dcmqi Resource Report Resource Website 1+ mentions |
dcmqi (RRID:SCR_016933) | dcmqi | data processing software, image processing software, software application, software library, software resource, software toolkit | Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. | DICOM, converter, medical, image, computing, quantitative, analysis, clinical, data, metadata, radiology, standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Harvard University; Cambridge; United States |
NCI U24 CA180918; NIBIB P41 EB01589; NIBIB P41 EB015902; NIBIB R01 EB014955 |
PMID:29092948 | Free, Available for download, Freely available, Tutorial available | biotools:dcmqi | https://github.com/QIICR/dcmqi, https://bio.tools/dcmqi | SCR_016933 | SciCrunch Registry | DICOM for Quantitative Imaging, The Digital imaging and Communications in Medicine for Quantitative Imaging, Digital imaging and Communications in Medicine for Quantitative Imaging, DCMQI | 2026-10-17 01:29:11 | 4 | ||||
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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 | SciCrunch Registry | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-10-17 01:29:11 | 25 | ||||
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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 | SciCrunch Registry | sashimi_plot | 2026-10-17 01:29:10 | 0 | |||||
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mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows. | proteomic, data, analysis, visualization, notebooking, mass, spectrometry, modification, gas, phase, fragmentation, behavior |
is listed by: OMICtools is related to: Python Programming Language |
Barr Program in Basic Research ; Dana-Farber Strategic Research Initiative ; Honorable Tina Brozman Foundation for Ovarian Cancer Research ; Michael J. Fox Foundation ; NCI CA042368; NCI CA178860; NCI CA188881 |
PMID:28763045 | Free, Available for download, Freely available | OMICS_26946 | https://omictools.com/mzstudio-tool | SCR_017088 | SciCrunch Registry | 2026-10-17 01:29:12 | 1 | ||||||
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Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | data analysis software, data processing software, software application, software resource | Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias. | quantifying, expression, transcript, RNAseq, data, correct, fragment, GC, content, bias |
is listed by: Debian is listed by: OMICtools has parent organization: Stony Brook University; New York; USA has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: Harvard University; Cambridge; Massachusetts |
Alfred P. Sloan Research ; Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NCI T32 CA009337; NHGRI R01 HG005220; NHGRI R01 HG007104; NHGRI R21 HG006913; NSF BIO-1564917; NSF CCF-1053918; NSF CCF-1256087; NSF EF-0849899 |
PMID:28263959 | Free, Available for download, Freely available | OMICS_09075 | https://github.com/COMBINE-lab/salmon, https://sources.debian.org/src/salmon/ | SCR_017036 | SciCrunch Registry | 2026-10-17 01:29:21 | 439 | ||||||
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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 | SciCrunch Registry | 2026-10-17 01:29:13 | 1 | |||||||||
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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 | SciCrunch Registry | 2026-10-17 01:29:48 | 6 | ||||||
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Structure Harvester Resource Report Resource Website 100+ mentions |
Structure Harvester (RRID:SCR_017636) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Visualizing, STRUCTURE, Evanno, method, collating, result, detection, genetic, group, fit, data, reformat |
is related to: University of California at Santa Cruz; California; USA is related to: University of California at Irvine; California; USA is related to: University of California at Los Angeles; California; USA works with: STRUCTURE |
NCI R21 CA135937; NCI U24 CA143858 |
DOI:10.1007/s12686-011-9548-7 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017636 | SciCrunch Registry | StructureHarvester | 2026-10-17 01:29:18 | 337 | |||||||
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data analysis software, data processing software, software application, software resource | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NCRR P41 RR011823; NHLBI R01 HL082747; NIA P30 AG013280; NIDDK R01 DK069386 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | SciCrunch Registry | 2026-10-17 01:28:48 | 3040 | ||||||||
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Tscratch Resource Report Resource Website 10+ mentions |
Tscratch (RRID:SCR_014282) | data analysis software, data processing software, image analysis software, software application, software resource, standalone software | Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze, wound, scratch, healing, assay, cell, migration, monolayer |
uses: MATLAB has parent organization: ETH Zurich; Zurich; Switzerland |
Austrian Science Foundation ; Cancer League Zurich ; Commission of the European Communities ; NCCR CO-ME ; NCI CA69184; Swiss National Fund |
PMID:19450233 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/cselab/TScratch | SCR_014282 | SciCrunch Registry | 2026-10-17 01:28:45 | 48 | |||||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | data analysis software, data processing software, software application, software resource | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | SciCrunch Registry | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-10-17 01:27:19 | 8 |
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