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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PAGODA Resource Report Resource Website |
PAGODA (RRID:SCR_017099) | data analysis software, software application, software resource, data processing software | Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells. | heterogeneity, transcriptional, detect, statistically, cell, classified, overlapping, gene, set, coordinated, variability |
is related to: pagoda2 has parent organization: Harvard University; Cambridge; United States |
Ellison Medical Foundation ; NSF NSF-14-532; NSF DGE1144152; NIMH U01 MH098977; NINDS R01 NS084398; NIA T32 AG00216 |
PMID:26780092 | Free, Available for download, Freely available | http://hms-dbmi.github.io/scde/index.html | SCR_017099 | Pathway And Gene set OverDispersion Analysis, pagoda | 2026-08-06 09:29:01 | 0 | ||||||
|
RaceID Resource Report Resource Website 10+ mentions |
RaceID (RRID:SCR_017045) | software resource, algorithm resource, data analysis software, data processing software, software application | Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows. | inference, cell, type, single, RNAseq, data, sequencing, rare, abundant, transcriptome, marker, gene, organ |
is listed by: OMICtools is related to: R Project for Statistical Computing is related to: CRAN works with: StemID |
European Research Council Advanced grant ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek Vici award |
PMID:26287467 PMID:27345837 |
Free, Available for download, Freely available | OMICS_12591, SCR_017243 | https://rdrr.io/cran/RaceID/, https://github.com/dgrun/RaceID3_StemID2 | SCR_017045 | RaceID3, RaceID2 | 2026-08-06 09:28:57 | 15 | |||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, software application, software resource, data processing software | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | 2026-08-06 09:29:00 | 354 | |||||||
|
PCAGO Resource Report Resource Website 1+ mentions |
PCAGO (RRID:SCR_017033) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options. | analysis, RNAseq, read, count, data, principal, component, analysis, PCA, agglomerative, clustering, normalization, filtering, gene, annotation, visualization | is listed by: OMICtools | Deutsche Forschungsgemeinschaft (DFG) ; International Leibniz Research School for Microbial and Biomolecular Interactions |
DOI:10.1101/433078 | Free, Freely available | OMICS_32232 | SCR_017033 | 2026-08-06 09:28:59 | 7 | |||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | data analysis software, software application, software resource, data processing software | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-08-06 09:29:04 | 2 | ||||||
|
Cell Ranger Resource Report Resource Website 500+ mentions |
Cell Ranger (RRID:SCR_017344) | data analysis software, software application, software resource, data processing software | Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics. | Analysis, process, chromium, singe, cell, RNA-seq, align, read, barcode, matrice, clustering, gene, expression, 10xGenomics |
is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology works with: Loupe Browser |
Restricted | SCR_017344 | 2026-08-06 09:29:02 | 611 | ||||||||||
|
PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-08-06 09:29:03 | 7 | ||||||||
|
HmtPhenome Resource Report Resource Website |
HmtPhenome (RRID:SCR_017289) | network graph visualization software, software resource, service resource, data or information resource, data processing software, data visualization software, software application, database | Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality. Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities. | mitochondria, variant, gene, function, phenotype, data |
uses: Human Phenotype Ontology uses: Ensembl uses: OMIM uses: Orphanet uses: DisGeNET has parent organization: University of Bari; Bari; Italy |
DOI:10.1101/660282 | Free, Freely available | SCR_017289 | 2026-08-06 09:29:01 | 0 | |||||||||
|
Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | software application, data processing software, data or information resource, software resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind | SCR_017339 | 2026-08-06 09:29:03 | 1 | |||||||||
|
Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | software resource, data analysis software, data processing software, data visualization software, software application | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Viertel Fellowship ; Victorian State Government Operational Infrastructure Support and Australian Government |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-08-06 09:29:03 | 23 | ||||||||
|
PIRATE Resource Report Resource Website 10+ mentions |
PIRATE (RRID:SCR_017265) | data analysis software, software application, software resource, data processing software | Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds. | Pangenome, clustering, genomics, bacteria, orthologue, gene, sequence, amino acid, nucleotide, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/598391 | Free, Available for download, Freely available | biotools:PIRAtE | https://bio.tools/PIRATE | SCR_017265 | Pangenome Iterative Refinement And Threshold Evaluation | 2026-08-06 09:29:02 | 18 | ||||||
|
4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | storage service resource, service resource, data repository, data or information resource, database | Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community. | Repository, chromatic, interaction, data, genomic, region, gene, name, detection, technology, curated | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | r3d100012282 | https://doi.org/10.17616/R3SH37 | SCR_017489 | 2026-08-06 09:29:05 | 10 | ||||||||
|
FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | software resource, data analysis software, data processing software, data visualization software, software application | Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. | Two, dimensional, data, reduction, single, cell, RNA seq, visualization, gene, expression, matrix, report, explore, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: University of California at Berkeley; Berkeley; USA |
National Institutes of Health NRSA Trainee appointment ; California Research Alliance by BASF ; NIMH U01 MH105979; NHGRI U01 HG007910 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-08-06 09:29:05 | 0 | ||||||
|
Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, web service, software resource | 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 |
NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-08-06 09:29:06 | 4 | ||||||
|
GO Gene Ontology Consortium and Knowledgebase Resource Report Resource Website 1+ mentions |
GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) | GOC | portal, consortium, data or information resource, organization portal | Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems. | Integrate, resource, model, organism, protein, database, gene, ontology, develope, cellular, system | NHGRI HG002273; NHGRI U24 HG012212 |
SCR_017505 | GO Consortium, Gene Ontology Consortium | 2026-08-06 09:29:08 | 8 | |||||||||
|
Nomenclature Resource Report Resource Website 1+ mentions |
Nomenclature (RRID:SCR_017511) | service resource, data or information resource | Authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows rules and guidelines established by International Committee on Standardized Genetic Nomenclature for Mice. | Mouse, gene, allele, strain, rule, guideline, nomenclature | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017511 | 2026-08-06 09:29:05 | 5 | ||||||||||
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clusterExperiment Resource Report Resource Website |
clusterExperiment (RRID:SCR_017439) | software resource, data analysis software, data processing software, data visualization software, software application | Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data. | Executing, evaluating, visualizing, clustering, experimental, data, single, cell, RNAseq, sequencing, gene, expression, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH U19 MH114830; NIMH U01 MH105979; Chan Zuckerberg Initiative ; ENS-CFM Data Science Chair |
PMID:30180157 | Free, Available for download, Freely available | SCR_017439 | 2026-08-06 09:29:04 | 0 | ||||||||
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Rotor-Gene 6000 series software Resource Report Resource Website 1+ mentions |
Rotor-Gene 6000 series software (RRID:SCR_017552) | data analysis software, software application, software resource, data processing software | Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC. | Rotor, Gene, 6000 Real Time, PCR machine, analysis, graphing, statistical, function | Free, Available for download, Freely available | https://www.baylor.edu/content/services/document.php/187886.pd | SCR_017552 | Rotor-Gene 6000 series software 1.7 | 2026-08-06 09:29:06 | 3 | |||||||||
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GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | data analysis software, software application, software resource, data processing software | Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. | Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Georgia Institute of Technology; Georgia; USA |
NHGRI HG000783 | PMID:25870408 | Restricted | biotools:GeneMarkS-t | https://bio.tools/GeneMarkS-T | SCR_017648 | 2026-08-06 09:29:07 | 113 | ||||||
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NYU Langone’s Advanced Rodent Transgenics Laboratory ART-Lab Core Facility Resource Report Resource Website 1+ mentions |
NYU Langone’s Advanced Rodent Transgenics Laboratory ART-Lab Core Facility (RRID:SCR_017692) | service resource, core facility, access service resource | Core offers services for researchers who want to apply advanced molecular genetic techniques in rodent models of physiology and disease. Provides expertise in generating novel mutant and transgenic mouse strains using genome engineering in mouse embryos and in embryonic stem cells (ESCs). Available technologies include:Generation of genome-edited mice by embryo pronuclear microinjection of DNA and genome editors (e.g., CRISPR/Cas9, site-specific recombinases) or traditional BAC transgenesis;Generation of genome-edited mice from mouse embryonic stem cells (mESCs) by chimeric blastocyst injection;Generation of genome-edited mice from mESCs by tetraploid blastocyst injection; Generation of mice from induced pluripotent stem cells;Assisted reproductive technologies; Sperm and embryo cryopreservation, storage and import/export;in vitro fertilization (IVF); Embryo rederivation technologies for animal import into barrier vivaria through quarantine. | Rodent, model, generation, mutant, mouse, strain, gene, targeting, embryonic, stem, cell, genetically, modified, CRISPR, Cas9, editing, in vivo, EZ-mouse model, in vitro, fertilization, cryopreservation, sperm, service, core, ABRF, USEDit |
is listed by: ABRF CoreMarketplace has parent organization: New York University School of Medicine; New York; USA |
Open | ABRF_822, ABRF_105, SCR_017925, SCR_017713 | https://coremarketplace.org/?FacilityID=822 | https://coremarketplace.org/?FacilityID=105, NYU School of Medicine Rodent Genetic Engineering Laboratory | SCR_017692 | NYU School of Medicine Rodent Genetic Engineering Laboratory Core Facility, Advanced Rodent Transgenics Laboratory (ART-Lab), NYU Langone Rodent Genetic Engineering Laboratory, New York University School of Medicine Langone Health Rodent Genetic Engineering Laboratory Core Facility, ART-Lab, RGEL, New York University Langone Medical Center Rodent Genetic Engineering Laboratory | 2026-08-06 09:29:08 | 4 |
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