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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Drop-seq tools Resource Report Resource Website 100+ mentions |
Drop-seq tools (RRID:SCR_018142) | data analysis software, data processing software, software application, software resource | Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Klarman Cell Observatory ; MGH Psychiatry Residency Research Program ; NHGRI P50 HG006193; NICHD F32 HD075541; NIMH R25 MH094612; NIMH U01 MH105960; NSF DMR 1310266; NSF DMR 1420570; NSF ECS 0335765; Simons Foundation ; Stanley Center for Psychiatric Research ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | SciCrunch Registry | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-11-07 12:00:52 | 112 | |||||||
|
MetaNeighbor Resource Report Resource Website 50+ mentions |
MetaNeighbor (RRID:SCR_016727) | data analysis software, data processing software, software application, software resource | Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting. | quantify, cell, type, replicability, dataset, access, cell, type, identity, functional, random, gene |
is used by: BICCN is listed by: Bioconductor is listed by: OMICtools |
Free, Available for download, Freely available | https://github.com/maggiecrow/MetaNeighbor, https://github.com/gillislab/MetaNeighbor | SCR_016727 | SciCrunch Registry | 2026-11-07 12:00:48 | 58 | |||||||||
|
OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | analysis service resource, data analysis service, data or information resource, production service resource, service resource, software resource, web application | Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | creating, metadata, analysis, annotated, gene, expression, data, compendia, human, mouse |
uses: Gene Expression Omnibus has parent organization: NIAID |
PMID:27323300 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016604 | SciCrunch Registry | OMics Compendia Commons | 2026-11-07 12:00:40 | 3 | |||||||
|
Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | data analysis software, data or information resource, data processing software, narrative resource, software application, software resource, training material, workflow | Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. | Epigenomic, analysis, pipeline, ChIP-Seq, RNA-Seq, data, Galaxy, Jupyter, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Estatal de Investigación of Spain SEV-2016-0672 (2017-2021) | Free, Available for download, Freely available | biotools:Epigenomics_Workflow_on_Galaxy_and_Jupyter | https://zenodo.org/record/3298029, https://bio.tools/Epigenomics_Workflow_on_Galaxy_and_Jupyter | SCR_017544 | SciCrunch Registry | REA pipeline | 2026-11-07 12:00:42 | 2 | ||||||
|
OpticalMapping.info Resource Report Resource Website |
OpticalMapping.info (RRID:SCR_017146) | data or information resource, portal, software resource, topical portal | Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data. | platform, tutorial, experimental, design, data, analysis, optical, mapping, structural, labelling, pattern, long, DNA, molecule, fluorescent, signal, capture | Free, Freely available | SCR_017146 | SciCrunch Registry | 2026-11-07 12:00:23 | 0 | |||||||||||
|
BeWith Resource Report Resource Website |
BeWith (RRID:SCR_016573) | BeWith | data analysis software, data processing software, software application, software resource | Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. | clustering, framework, identify, module, mutation, interaction, pattern, gene, cancer | Naomi Kadar award ; NIH |
DOI:10.1371/journal.pcbi.1005695 | Free, Available for download, Freely available | SCR_016573 | SciCrunch Registry | BEtweenWITHin, Between-Within, BeWith | 2026-11-07 12:00:51 | 0 | |||||||
|
GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data access protocol, software resource, web service | Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
Free, Freely available | SCR_016297 | SciCrunch Registry | , GLIMMPSE Version 3 | 2026-11-07 12:00:40 | 9 | ||||||||
|
factoextra Resource Report Resource Website 100+ mentions |
factoextra (RRID:SCR_016692) | data analysis software, data processing software, data visualization software, software application, software resource | R package from CRAN to extract and visualize the results of multivariate data analysis. | extract, visualize, multivariate, data, analysis |
is affiliated with: R Project for Statistical Computing is affiliated with: CRAN |
Free, Available for download, Freely available | https://rpkgs.datanovia.com/factoextra/index.html | SCR_016692 | SciCrunch Registry | 2026-11-07 12:00:41 | 117 | |||||||||
|
Gsnap2Augustus Resource Report Resource Website 1+ mentions |
Gsnap2Augustus (RRID:SCR_017555) | simulation software, software application, software resource | Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap. | Generate, hint, Augustus, gene, prediction, mapping, Gsnap |
uses: GSNAP works with: Augustus |
Free, Available for download, Freely available | SCR_017555 | SciCrunch Registry | 2026-11-07 12:00:52 | 1 | ||||||||||
|
Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | data analysis software, data processing software, software application, software resource | Software tool for de novo transcriptome assembly from RNA-Seq data. | de novo, transcriptome, assembly, RNAseq, data |
has parent organization: University of Washington; Seattle; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Stanford University; Stanford; California |
NHGRI ; NSF Center for Science of Information ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | SciCrunch Registry | 2026-11-07 12:00:52 | 2 | ||||||||
|
NiMARE Resource Report Resource Website 10+ mentions |
NiMARE (RRID:SCR_017398) | NiMARE | data analysis software, data processing software, software application, software resource | Software Python package for coordinate and image based meta analysis of neuroimaging data. | Coordinate, image, based, meta, analysis, neuroimaging, data |
uses: PyMARE is used by: Neurosynth Compose |
Free, Available for download, Freely available | https://nimare.readthedocs.io/en/latest/ | SCR_017398 | SciCrunch Registry | Neuroimaging Meta Analysis Research Environment, Neuroimaging Meta-Analysis Research Environment | 2026-11-07 12:00:23 | 17 | |||||||
|
NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | data analysis software, data processing software, simulation software, software application, software resource | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | SciCrunch Registry | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-11-07 12:00:52 | 45 | ||||||||
|
ngsRelate Resource Report Resource Website 1+ mentions |
ngsRelate (RRID:SCR_016588) | data analysis software, data processing software, software application, software resource | Software tool for estimating pairwise relatedness from next-generation sequencing data. | estimating, pairwise, relatedness, next, generation, sequencing, data, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
Danish Council for Independent Research ; Danish National Research Foundation |
PMID:26323718 | Free, Available for download, Freely available | biotools:ngsRelateV2, biotools:ngsrelate | https://bio.tools/ngsRelateV2, https://bio.tools/ngsrelate | http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694 | SCR_016588 | SciCrunch Registry | ngsRelateV2 | 2026-11-07 12:00:47 | 6 | ||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data analysis software, data processing software, data visualization software, software application, software resource | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
BMBF ; German Cancer Research Center-Heidelberg Center for Personalized Oncology |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | SciCrunch Registry | 2026-11-07 12:00:52 | 3949 | ||||||
|
Deltagraph Resource Report Resource Website |
Deltagraph (RRID:SCR_018084) | data analysis software, data analytics software, data processing software, data visualization software, software application, software resource | Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities. | Data, statistic, visualization, chart selection, graph, analysis, Red Rock Software Inc. | Restricted | SCR_018084 | SciCrunch Registry | 2026-11-07 12:00:50 | 0 | |||||||||||
|
Computational Structural Biology Toolbox Resource Report Resource Website |
Computational Structural Biology Toolbox (RRID:SCR_016065) | CSB | software library, software resource, software toolkit | Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses. | software, library, Python, reading, storing, analysis, biomolecular, variety, statistical, analysis, bioinformatic |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft (DFG) grant HA 5918/1-1; Max Planck Society |
PMID:22942023 | Free, Available for download | OMICS_09827 | https://sources.debian.org/src/csb/ | SCR_016065 | SciCrunch Registry | Computational Structural Biology Toolbox (CSB), CSB Toolbox | 2026-11-07 12:00:51 | 0 | ||||
|
Seurat Resource Report Resource Website 10000+ mentions |
Seurat (RRID:SCR_016341) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is used by: scSidekick is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | SciCrunch Registry | 2026-11-07 12:00:47 | 11480 | |||||||
|
SWISS-MODEL Resource Report Resource Website 1000+ mentions |
SWISS-MODEL (RRID:SCR_018123) | data access protocol, data or information resource, service resource, software resource, web service | Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists. | 3D protein structure, homology modeling server, protein modeling, structural bioinformatics, automated comparative modeling, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: Swiss-PdbViewerDeepViewv4.0 has parent organization: University of Basel; Basel; Switzerland provides: SWISS-MODEL Repository |
PMID:12824332 | Free, Freely available | biotools:swiss-model_workspace, biotools:swiss_model | https://bio.tools/swiss_model, https://bio.tools/swiss-model_workspace | SCR_018123 | SciCrunch Registry | 2026-11-07 12:00:24 | 4218 | |||||||
|
LTRpred Resource Report Resource Website 1+ mentions |
LTRpred (RRID:SCR_017031) | data analysis software, data analytics software, data processing software, software application, software resource | Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format. | LTR, retrotransposon, prediction, genome, assembly, functional, annotation | is related to: R Project for Statistical Computing | Free, Available to download, Freely available | https://hajkd.github.io/LTRpred/ | SCR_017031 | SciCrunch Registry | LTRpred(ict) | 2026-11-07 12:00:23 | 6 | ||||||||
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NIAID Overview of Coronaviruses Resource Report Resource Website 1+ mentions |
NIAID Overview of Coronaviruses (RRID:SCR_018290) | data or information resource, funding resource, portal, topical portal | Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses. | Coronavirus, COVID-19, data, infectious disease, NIAID |
is listed by: Data and Computational Resources to Address COVID-19 is related to: NIAID |
COVID-19 | NIAID | Free, Freely available | SCR_018290 | SciCrunch Registry | 2026-11-07 12:00:53 | 4 |
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