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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-05 06:30:08 | 117 | |||||||||
|
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 | Neuroimaging Meta Analysis Research Environment, Neuroimaging Meta-Analysis Research Environment | 2026-09-05 06:30:08 | 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 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-09-05 06:30:08 | 45 | ||||||||
|
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 | 2026-09-05 06:30:09 | 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 | Computational Structural Biology Toolbox (CSB), CSB Toolbox | 2026-09-05 06:30:07 | 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 | 2026-09-05 06:30:07 | 11480 | |||||||
|
IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | alignment software, analysis service resource, data or information resource, data processing software, image analysis software, portal, production service resource, service resource, software application, software resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
CNRS ; GENCI ; MESR ; NHMRC ; Université Montpellier 2 ; France |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-09-05 06:30:09 | 15 | |||||
|
Biocode Commons Resource Report Resource Website |
Biocode Commons (RRID:SCR_024553) | data or information resource, portal, topical portal | Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO. | Biological Collections Ontology, Biological Collections Ontology development, genomic observations, collection, analysis, publication, standards community, |
is listed by: DataCite is listed by: University of California; California; USA has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.7286 | SCR_024553 | 2026-09-05 06:30:32 | 0 | |||||||||
|
GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | data access protocol, data or information resource, database, software resource, web service | Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. | database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics |
is listed by: OMICtools is related to: University of British Columbia; British Columbia; Canada |
Canadian Foundation for Innovation infrastructure ; CIHR ; NIH MH111099; NSERC Discovery Grant |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack, https://omictools.com/gotrack-tool | SCR_016399 | 2026-09-05 06:28:08 | 1 | |||||||
|
RELION Resource Report Resource Website 100+ mentions |
RELION (RRID:SCR_016274) | data analysis software, data processing software, software application, software resource, standalone software | Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy. | cryo, cryogenic, cryo em, determination, analysis, bayesian, statistic, map, maximum a posteriori, electron, cryomicroscopy |
is listed by: Debian is listed by: OMICtools |
UK Medical Research Council | PMID:23000701 | Free, Available for download, Tutorial available | OMICS_15597 | https://sources.debian.org/src/relion-bin+mpi+gui/ | SCR_016274 | RELION, REgularised LIkelihood OptimisatioN, RELION-3 | 2026-09-05 06:28:06 | 440 | |||||
|
Vensim Resource Report Resource Website 10+ mentions |
Vensim (RRID:SCR_016394) | simulation software, software application, software resource | Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models. | performance, system, Ventana Systems Inc, model, modelling, analysis | Commercially available, Available for purchase | SCR_016394 | 2026-09-05 06:28:08 | 14 | |||||||||||
|
OmicsBean Resource Report Resource Website 100+ mentions |
OmicsBean (RRID:SCR_016322) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users. | GeneForHealth Biotech Inc (GFK), data, analysis, genome, proteome, metabolome, network, molecular, mechanism, model, collect, store, analytic, multi, omic | Commercially available, Demo available | SCR_016322 | 2026-09-05 06:28:06 | 189 | |||||||||||
|
ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-09-05 06:28:07 | 10 | ||||||||||
|
MxPro QPCR Resource Report Resource Website 500+ mentions |
MxPro QPCR (RRID:SCR_016375) | data analysis software, data processing software, software application, software resource | Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pcr, qpcr, polymerase, qualitative, analysis, nucleic, acid, gene | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016375 | MxPro QPCR Software | 2026-09-05 06:28:07 | 543 | ||||||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-09-05 06:28:08 | 5 | |||||||
|
Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Epigenome Programme DEEP 01KU1216G; German Research Foundation SFB 992 |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-09-05 06:28:07 | 2806 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-09-05 06:28:07 | 2 | |||||
|
migec Resource Report Resource Website 10+ mentions |
migec (RRID:SCR_016337) | MIGEC | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | European Regional Development Fund ; Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-09-05 06:28:07 | 11 | |||||||
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FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | data analysis software, data processing software, image analysis software, software application, software resource | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | 2026-09-05 06:28:07 | 16 | |||||||||||
|
star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | alignment software, data processing software, image analysis software, software application, software resource | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | AMEDD Advanced Medical Technology Initiative ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-09-05 06:28:06 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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