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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | data analysis software, data processing software, data visualization software, software application, software resource | 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 ; Victorian State Government Operational Infrastructure Support and Australian Government ; Viertel Fellowship |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-09-12 12:58:52 | 23 | ||||||||
|
Functional Annotation Resource Report Resource Website 1+ mentions |
Functional Annotation (RRID:SCR_017519) | service resource | MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO). | MGI, GO, functional, annotation, mouse, gene, product, Gene Ontology |
uses: Gene Ontology has parent organization: Mouse Genome Informatics (MGI) |
Free, Freely available | SCR_017519 | 2026-09-12 12:58:53 | 4 | ||||||||||
|
4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | data or information resource, data repository, database, service resource, storage service resource | 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 | 2026-09-12 12:58:53 | 11 | ||||||||
|
GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:55 | 172 | ||||||
|
FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | data analysis software, data processing software, data visualization software, software application, software resource | 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 |
California Research Alliance by BASF ; National Institutes of Health NRSA Trainee appointment ; NHGRI U01 HG007910; NIMH U01 MH105979 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-09-12 12:58:53 | 0 | ||||||
|
Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, web service | 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 |
NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-09-12 12:58:54 | 6 | ||||||
|
GO Gene Ontology Consortium and Knowledgebase Resource Report Resource Website 10+ mentions |
GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) | GOC | consortium, data or information resource, organization portal, 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 | 2026-09-12 12:58:53 | 10 | |||||||||
|
Nomenclature Resource Report Resource Website 1+ mentions |
Nomenclature (RRID:SCR_017511) | data or information resource, service 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 | 2026-09-12 12:58:53 | 5 | ||||||||||
|
Knockout Mouse Project Repository at JAX Resource Report Resource Website |
Knockout Mouse Project Repository at JAX (RRID:SCR_017512) | data or information resource | Information from JAX about their contributions to KOMP project coordinated by International Mouse Phenotyping Consortium. National Institutes of Health has funded three KOMP2 centers in United States, including one at Jackson Laboratory, to work together on task of producing and phenotyping mice to establish resource of knockout mice and related database of gene function. | KOMP, JAX, knockout, mice, data, gene, function, phenotype |
is related to: International Mouse Phenotyping Consortium (IMPC) is related to: JAX Mice and Services has parent organization: Knockout Mouse Project |
Free, Freely available | https://www.jax.org/mouse-search?searchTerm=repository | SCR_017512 | 2026-09-12 12:58:53 | 0 | |||||||||
|
Rotor-Gene 6000 series software Resource Report Resource Website 1+ mentions |
Rotor-Gene 6000 series software (RRID:SCR_017552) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:54 | 3 | |||||||||
|
SL-quant Resource Report Resource Website 1+ mentions |
SL-quant (RRID:SCR_016205) | SLQ | data analysis software, data processing software, sequence analysis software, software application, software resource | Source code for a bash pipeline that quantifies splice-leader (SL) trans-splicing events by genes in the nematode C. elegans. It is designed to work downstream of read mapping and takes the reads left unmapped as primary input. | RNA-seq, trans-splicing, pipeline, c elegans, bash, nematode, read, mapping, gene |
requires: cutadapt requires: SAMTOOLS requires: HISAT2 requires: BEDTools requires: Picard requires: featureCounts |
FNRS-FRIA | Free, Available for download | SCR_016205 | 2026-09-12 12:58:36 | 1 | ||||||||
|
HumanNet Resource Report Resource Website 100+ mentions |
HumanNet (RRID:SCR_016146) | data analysis software, data or information resource, data processing software, database, software application, software resource, web application | Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes. | probability, gene, protein, encode, statistic, likelihood, network, bayesian, omic, pathway, guilt by association, FASEB list |
has parent organization: University of Texas at Austin; Texas; USA has parent organization: Yonsei University; Seoul; South Korea |
Korean government (MEST) 2010-0017649; National Research Foundation of Korea (NRF) ; Packard Foundations ; POSCO TJ ; U.S. Army Research 58343-MA; Welch F1515; Wellcome Trust 076113; Wellcome Trust 085475 |
Freely available | SCR_016146 | 2026-09-12 12:58:35 | 135 | |||||||||
|
MultiNet Resource Report Resource Website 10+ mentions |
MultiNet (RRID:SCR_016149) | software resource | Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network. | network, integration, human, protein, interactome, gene, interaction | PMID:23505346 | Free, Available for download | SCR_016149 | 2026-09-12 12:58:36 | 14 | ||||||||||
|
Clinker Resource Report Resource Website 100+ mentions |
Clinker (RRID:SCR_016140) | data processing software, data visualization software, software application, software resource | Software for a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc). They can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz. | fusion, chimeric, gene, bioinformatics, transcriptome, viewer, plotting, graph, visualization | Murdoch Children's Research Institute | Free, Available for download | SCR_016140 | Clinker - Fusion Super Transcript generator and Plotter | 2026-09-12 12:58:35 | 364 | |||||||||
|
L1000 Characteristic Direction Signature Search Engine Resource Report Resource Website 1+ mentions |
L1000 Characteristic Direction Signature Search Engine (RRID:SCR_016177) | L1000CDS2 | data access protocol, data or information resource, data set, database, service resource, software resource, web service | LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction. | signature, gene, dataset, ligand, characteristic, expression, benchmark |
is related to: LINCS Joint Project - Breast Cancer Network Browser has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U54 CA189201; NHLBI U54 HL127624 |
PMID:28413689 | Free, Freely available | SCR_016177 | 2026-09-12 12:58:36 | 8 | |||||||
|
Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-09-12 12:58:36 | 142 | |||||||||
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AIIA-GMT Resource Report Resource Website |
AIIA-GMT (RRID:SCR_016397) | data access protocol, software application, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 14, 2018. An XML-RPC client of a web-service server which provides the service to recognize named entities in the biomedical articles. It is Gene Mention Tagger (GMT) for Biological Text Mining. | biomedical, article, gene, mention, tagger, biological, text, mining, research, journal | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016397 | 2026-09-12 12:58:39 | 0 | |||||||||||
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Phenocarta Resource Report Resource Website 1+ mentions |
Phenocarta (RRID:SCR_016273) | data analysis software, data or information resource, data processing software, database, software application, software resource | Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data. | phenotype, meta, analysis, genome, gene, expression |
is related to: Gemma has parent organization: University of British Columbia; British Columbia; Canada |
PMID:22782548 | Free, Freely available | http://pavlab.msl.ubc.ca/software-and-resources/ | SCR_016273 | Phenocarta | 2026-09-12 12:58:37 | 2 | |||||||
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AspireDB Resource Report Resource Website |
AspireDB (RRID:SCR_016272) | data analysis software, data processing software, software application, software resource, web application | Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes. | gene, cnv, snv, indel, phenotype, analysis, variant | BC Knowledge Development Fund ; Canadian Foundation for Innovation |
Account required, Freely available | https://github.com/ppavlidis/aspiredb, http://pavlab.msl.ubc.ca/software-and-resources/ | SCR_016272 | 2026-09-12 12:58:37 | 0 | |||||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | Alfred P. Sloan Foundation Research Fellowship ; NIH DP2 HD088158 |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-09-12 12:58:38 | 227 |
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