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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | web application, service resource, production service resource, analysis service resource, software resource, data analysis service | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele, https://bio.tools/nephele | SCR_016595 | 2026-08-12 10:51:33 | 36 | ||||||
|
Cyflogic Resource Report Resource Website 10+ mentions |
Cyflogic (RRID:SCR_016635) | software toolkit, software application, data processing software, software resource, data analysis software | Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics. | flow, cytometry, data, analysis, CyFlo Ltd., dot, plot, histogram, statistics | PMID:23839300 | Commercially available, Free for non-commercial research use only and not for use in diagnostic or therapeutic procedures | SCR_016635 | 2026-08-12 10:51:34 | 27 | ||||||||||
|
scanpy Resource Report Resource Website 100+ mentions |
scanpy (RRID:SCR_018139) | data processing software, data analysis software, software resource, software application | Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time. | Large scale, single cell, gene expression, data analysis, R, pre processing, visualization, graph drawing, diffusion map, clustering, marker gene, differential expression test, bio.tools |
uses: BBKNN is used by: triku is used by: MUON is listed by: Debian is listed by: bio.tools is related to: Anndata has plug in: infercnvpy |
Helmholtz Postdoc Programme ; German Research Foundation |
PMID:29409532 | Free, Available for download, Freely available | biotools:scanpy, BioTools:scanpy | https://icb-scanpy.readthedocs-hosted.com/en/stable/, https://bio.tools/scanpy, https://bio.tools/scanpy, https://bio.tools/scanpy | SCR_018139 | Single Cell Analysis in Python | 2026-08-12 10:52:03 | 256 | |||||
|
Indiana University Center for Genomics and Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Indiana University Center for Genomics and Bioinformatics Core Facility (RRID:SCR_017165) | CGB | data or information resource, access service resource, core facility, service resource | CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis. | ABRF, genomic services, DNA/RNA extraction, library preparation, next-generation sequencing, bioinformatic analysis, |
is listed by: ABRF CoreMarketplace has parent organization: Indiana University Bloomington; Indiana; USA |
Restricted | SCR_025534, ABRF_2841 | https://indianactsi.org/servicecores/core/20/, https://coremarketplace.org/?FacilityID=2841&citation=1 | SCR_017165 | Indiana University Bloomington Center for Genomics and Bioinformatics | 2026-08-12 10:51:42 | 3 | ||||||
|
NCBI Virus Resource Report Resource Website 50+ mentions |
NCBI Virus (RRID:SCR_018253) | portal, data or information resource, topical portal, data access protocol, software resource, web service | Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories. | Viral sequence data, viral data retrival, viral data analysis, viral data display, curated virus sequence, data set |
is related to: RefSeq is related to: GenBank |
PMID:27899678 | Free, Freely available | SCR_018253 | National Center for Biotechnology Information Virus | 2026-08-12 10:52:04 | 76 | ||||||||
|
NEB Tm calculator Resource Report Resource Website 1+ mentions |
NEB Tm calculator (RRID:SCR_017969) | service resource, software resource, data access protocol, web service | Calculator to estimate appropriate annealing temperature when using NEB PCR products.Tm calculator provided by New England Biolabs. | Calculate, estimate, annealing, temperature, PCR, product, New England Biolabs Inc., NEBtool | SCR_017969 | 2026-08-12 10:52:00 | 3 | ||||||||||||
|
PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | service resource, data or information resource, production service resource, database, software resource, analysis service resource, data access protocol, web service | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | PAirwise Sequence Comparison | 2026-08-12 10:51:34 | 6 | ||||||
|
Singularity Registry Resource Report Resource Website 1+ mentions |
Singularity Registry (RRID:SCR_016249) | sregistry | application programming interface, web application, data storage software, software application, data processing software, data access protocol, software resource, data distribution software | Web application and registry for institutional deployment of Singularity containers. | containers, singularity, containers, linux, python, django, storage | is related to: Singularity Hub | PMID:28494014 | Open source, Freely available | SCR_016249 | Singularity Registry Server | 2026-08-12 10:51:31 | 2 | |||||||
|
SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | data or information resource, database, data access protocol, software resource, web service | Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. | collection, regulatory, single, polymorphism, SNP, affecting, predicted, transcription, factor, binding, site, affinity, data, human, nucleotide, genome | Swiss National Science Foundation ; Swiss Institute of Bioinformatics |
PMID:27899579 | Free, Freely available | SCR_016885 | Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS | 2026-08-12 10:51:37 | 8 | |||||||
|
Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility Resource Report Resource Website 1+ mentions |
Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility (RRID:SCR_017172) | SCTC, JHMI, JHU | service resource, production service resource, core facility, analysis service resource, access service resource | Core provides assistance with Single Cell RNA and DNA Sequencing, Spatial Transcriptomics, Next-Generation Sequencing libraries. | single, cell, spatial, omics, next, generation, sequencing, DNA, RNA | Restricted | SCR_017172 | , Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core | 2026-08-12 10:51:38 | 1 | |||||||||
|
Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | project portal, portal, data or information resource, database, data set | Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data. | Spienza University of Rome, Cineca, RNA seq, transcriptome, data, brain, mouse, stress, gene, expresison | Free, Available for download, Freely available | SCR_017572 | 2026-08-12 10:51:46 | 1 | |||||||||||
|
Drop-seq tools Resource Report Resource Website 100+ mentions |
Drop-seq tools (RRID:SCR_018142) | data processing software, data analysis software, software resource, software application | 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 |
Stanley Center for Psychiatric Research ; MGH Psychiatry Residency Research Program ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award ; Simons Foundation ; NHGRI P50 HG006193; Klarman Cell Observatory ; NIMH U01 MH105960; NIMH R25 MH094612; NICHD F32 HD075541; NSF ECS 0335765; NSF DMR 1310266; NSF DMR 1420570 |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-08-12 10:52:03 | 112 | |||||||
|
MetaNeighbor Resource Report Resource Website 50+ mentions |
MetaNeighbor (RRID:SCR_016727) | data processing software, data analysis software, software resource, software application | 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 | 2026-08-12 10:51:30 | 58 | |||||||||
|
OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | web application, service resource, data or information resource, production service resource, analysis service resource, software resource, data analysis service | 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 | 2026-08-12 10:51:28 | 3 | |||||||
|
Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | data or information resource, narrative resource, workflow, software application, training material, data processing software, software resource, data analysis software | 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 | 2026-08-12 10:51:45 | 2 | ||||||
|
IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | portal, service resource, data or information resource, production service resource, image analysis software, software application, data processing software, alignment software, analysis service resource, 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 |
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 | 2026-08-12 10:52:03 | 15 | |||||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data processing software, data analysis software, software resource, software application | 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., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016297 | , GLIMMPSE Version 3 | 2026-08-12 10:51:23 | 9 | ||||||||
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factoextra Resource Report Resource Website 100+ mentions |
factoextra (RRID:SCR_016692) | data visualization software, software application, data processing software, software resource, data analysis software | 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 | 2026-08-12 10:51:30 | 117 | |||||||||
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Gsnap2Augustus Resource Report Resource Website 1+ mentions |
Gsnap2Augustus (RRID:SCR_017555) | simulation software, software resource, software application | 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 | 2026-08-12 10:51:49 | 1 | ||||||||||
|
Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | data processing software, data analysis software, software resource, software application | 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 |
NSF Center for Science of Information ; NHGRI ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | 2026-08-12 10:51:35 | 2 |
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