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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | software resource, service resource, production service resource, data analysis service, data or information resource, web application, analysis service resource | 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 | OMics Compendia Commons | 2026-08-06 09:28:54 | 1 | |||||||
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Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | workflow, software resource, data analysis software, data or information resource, data processing software, software application, training material, narrative resource | 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 | REA pipeline | 2026-08-06 09:29:08 | 2 | ||||||
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OpticalMapping.info Resource Report Resource Website |
OpticalMapping.info (RRID:SCR_017146) | portal, topical portal, data or information resource, software resource | 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 | 2026-08-06 09:28:59 | 0 | |||||||||||
|
IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | software resource, image analysis software, alignment software, service resource, production service resource, data or information resource, data processing software, portal, software application, analysis service 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 |
NHMRC ; MESR ; CNRS ; Université Montpellier 2 ; France ; GENCI |
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 | 2026-08-06 09:29:18 | 11 | |||||
|
factoextra Resource Report Resource Website 50+ mentions |
factoextra (RRID:SCR_016692) | software resource, data analysis software, data processing software, data visualization software, software application | 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 | 2026-08-06 09:28:53 | 89 | |||||||||
|
NiMARE Resource Report Resource Website 10+ mentions |
NiMARE (RRID:SCR_017398) | NiMARE | data analysis software, software application, software resource, data processing software | 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 | 2026-08-06 09:29:04 | 13 | |||||||
|
NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | software resource, data analysis software, data processing software, software application, simulation software | 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 | 2026-08-06 09:28:59 | 42 | ||||||||
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Deltagraph Resource Report Resource Website |
Deltagraph (RRID:SCR_018084) | software resource, data analytics software, data analysis software, data processing software, data visualization software, software application | 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 | 2026-08-06 09:29:19 | 0 | |||||||||||
|
Seurat Resource Report Resource Website 5000+ mentions |
Seurat (RRID:SCR_016341) | software resource, data analysis software, software toolkit, data processing software, software application | 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 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 | 2026-08-06 09:28:53 | 9395 | |||||||
|
Bamboo DiRT Resource Report Resource Website 1+ mentions |
Bamboo DiRT (RRID:SCR_002556) | Bamboo DiRT | database, data or information resource | Registry of digital research tools for scholarly use that makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analysis, registry | is listed by: FORCE11 | Andrew W. Mellon Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156034 | http://www.force11.org/node/4756 | SCR_002556 | Bamboo Dirt registry of digital research tools for scholarly use, Bamboo Digital Research Tools | 2026-08-06 09:25:40 | 1 | |||||
|
VIPERdb Resource Report Resource Website 50+ mentions |
VIPERdb (RRID:SCR_002853) | database, data or information resource | Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | exploration, analysis, capsid, computational, convention, database, icosahedral, structural, structure, system, virus, visual, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Scripps Research Institute |
PMID:33313778 PMID:30265627 |
Free, Freely available | nif-0000-25311, r3d100012362, nif-0000-03630, biotools:viperdb, SCR_007970 | https://bio.tools/viperdb, https://doi.org/10.17616/R3HT0Q | SCR_002853 | Virus Particle ExploreR | 2026-08-06 09:25:44 | 59 | ||||||
|
SHEsis: Analysis Tools For Random Samples Resource Report Resource Website 50+ mentions |
SHEsis: Analysis Tools For Random Samples (RRID:SCR_002958) | SHEsis | data analysis service, production service resource, analysis service resource, service resource | A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. | analysis, disequilibrium, haplotype, genetic, association, polymorphism, locus, linkage disequilibrium | has parent organization: Shanghai Jiao Tong University; Shanghai; China | Major State Basic Research Development program of China ; National High Technology Research and Development Program of China |
PMID:19290020 PMID:15740637 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30105 | http://analysis.bio-x.cn/myAnalysis.php | SCR_002958 | 2026-08-06 09:25:45 | 80 | |||||
|
CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | data analysis software, software application, software resource, data processing software | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | CFX Manager software | 2026-08-06 09:29:04 | 489 | |||||||||
|
ape Resource Report Resource Website 10+ mentions |
ape (RRID:SCR_017343) | data analysis software, software application, software resource, data processing software | Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R. | analysis, phylogenetics, evolution, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: CRAN |
PMID:30016406 PMID:14734327 PMID:22495750 |
Free, Available for download, Freely available | biotools:ape | https://cran.r-project.org/web/packages/ape/ape.pdf, http://ape-package.ird.fr/, https://bio.tools/ape | SCR_017343 | ape 3.0, ape 5.0, Analysis of Phylogenetics and Evolution | 2026-08-06 09:29:05 | 42 | ||||||
|
Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | data analysis software, software application, software resource, data processing software | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-08-06 09:29:03 | 15 | |||||||||
|
SeQuiLa Resource Report Resource Website 1+ mentions |
SeQuiLa (RRID:SCR_017220) | data analysis software, software application, software resource, data processing software | Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals. | genomic, intervals, querying, processing, Apache, Spark, SQL, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Warsaw University of Technology; Warsaw; Poland |
National Science Center ; Polish budget funds for science |
PMID:30428005 | Free, Available for download, Freely available | biotools:SeQuiLa-cov | http://biodatageeks.org/sequila/, https://bio.tools/SeQuiLa-cov | SCR_017220 | 2026-08-06 09:29:02 | 1 | ||||||
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Computational Suite for Bioinformaticians and Biologists Resource Report Resource Website 1+ mentions |
Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) | CSBB | data analysis software, software application, software resource, data processing software | Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments. | analysis, sequencing, data, command, line, expression, normalization, convert | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_17554 | https://github.com/csbbcompbio | SCR_017234 | CSBB-v3.0, CSBB-v1.0, CSBB-v2.0, Computational Suite for Bioinformaticians and Biologists | 2026-08-06 09:29:03 | 6 | ||||||
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Rice_HxD_Recovery_Metabolomics Resource Report Resource Website 1+ mentions |
Rice_HxD_Recovery_Metabolomics (RRID:SCR_017204) | source code, software resource, data analysis software, data processing software, data visualization software, software application | Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress. | analysis, GC-MS, data, rice, sample, statistics, workflow | Free, Available for download, Freely available | SCR_017204 | 2026-08-06 09:29:02 | 1 | |||||||||||
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redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | software resource, service resource, production service resource, data analysis software, data analysis service, data processing software, software application, analysis service resource | Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data. | microbiome, feature, identify, characterize, analysis, metadata, sample, data | PMID:31239397 | Free, Available for download, Freely available | SCR_017285 | 2026-08-06 09:29:04 | 5 | ||||||||||
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PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data analysis software, software application, software resource, data processing software | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-08-06 09:29:03 | 15 |
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