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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data analysis software, data processing software, network analysis software, software application, software resource, software toolkit | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-09-19 12:53:56 | 0 | |||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, service resource, software resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCATS UL1 TR001114; NCI K22 CA188163; NHGRI U01 HG006476; NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info, https://bio.tools/mygene.info, https://bio.tools/mygene.info | SCR_018660 | 2026-09-19 12:53:56 | 34 | ||||||
|
RatsPub Resource Report Resource Website |
RatsPub (RRID:SCR_018905) | data access protocol, software application, software resource, text-mining software, web service | Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords. | Literature mining, addiction gene, PubMed abstract, gene, addiction, addiction relationship, neurogenetics | NIDA P30 DA044223; NIDA U01 DA047638 |
Free, Freely available | https://github.com/chen42/ratspub | SCR_018905 | rats.pub, Rats.pub, Relationship with Addiction Through Searches of PubMed | 2026-09-19 12:54:00 | 0 | ||||||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, service resource, software resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626; NIGMS ; NIH Common Fund |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-09-19 12:54:01 | 7 | |||||||
|
CluePedia Cytoscape plugin Resource Report Resource Website 100+ mentions |
CluePedia Cytoscape plugin (RRID:SCR_015784) | data analysis software, data processing software, data visualization software, software application, software resource | Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments. | cytoscape, cluepedia, search tool, marker, pathway, experimental data, in silico data, linear dependence, gene, protein, miRNA | is a plug in for: Cytoscape | INCa ; Canceropole Ile de France ; INSERM ; MedImmune ; Qatar National Research Fund NPRP09-1174-3-291; European Commission 7FP Geninca 202230); LabEx Immuno-Oncology |
PMID:23325622 | Free for non-profits, Free for academic use, Available for download, Commercially available, Available for purchase | SCR_015784 | CluePedia: A ClueGO plugin, CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data | 2026-09-19 12:53:12 | 193 | |||||||
|
Piggy Resource Report Resource Website 10+ mentions |
Piggy (RRID:SCR_015941) | data analysis software, data processing software, software application, software resource | Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary). | intergenic, region, bacterial, analysis, gene, genome, assembly | Medical Research Council | Free, Available for download | SCR_015941 | 2026-09-19 12:53:14 | 32 | ||||||||||
|
UK Brain Expression Consortium Resource Report Resource Website 1+ mentions |
UK Brain Expression Consortium (RRID:SCR_015889) | UKBEC | consortium, data or information resource, organization portal, portal | Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders. | neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expression | is parent organization of: Braineac | SCR_015889 | 2026-09-19 12:53:14 | 3 | ||||||||||
|
Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-09-19 12:53:15 | 722 | |||||||
|
National Gene Vector Laboratories Resource Report Resource Website 1+ mentions |
National Gene Vector Laboratories (RRID:SCR_015944) | NGVL | data or information resource, portal, topical portal | The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies. | gene, therapy, manufacturing, toxicology, human, research, vector, transfer, study | is used by: Adobe Illustrator | NIH | SCR_015944 | 2026-09-19 12:53:14 | 2 | |||||||||
|
EnrichmentMap Resource Report Resource Website 500+ mentions |
EnrichmentMap (RRID:SCR_016052) | data processing software, data visualization software, software application, software resource, source code | Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together. | cytoscape, functional, visualization, enrichment, gene, mapping, genome, pathway, network, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: Cytoscape |
Canada Foundation for Innovation ; Heart and Stroke Foundation of Canada ; NHGRI P41 HG04118; Ontario Genomics Institute ; Ontario Research Fund (ORF) |
PMID:21085593 | biotools:enrichmentmap | https://github.com/BaderLab/EnrichmentMapApp, https://bio.tools/enrichmentmap | SCR_016052 | 2026-09-19 12:53:16 | 590 | |||||||
|
YAMP Resource Report Resource Website 1+ mentions |
YAMP (RRID:SCR_016236) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability. | metagenomics, reproducibility, workflow, containerization, sequencing, gene, rna, annotating, portable, data, process | Free, Available for download | SCR_016236 | YAMP: Yet Another Metagenomic Pipeline, Yet Another Metagenomic Pipeline (YAMP), Yet Another Metagenomic Pipeline | 2026-09-19 12:53:19 | 8 | ||||||||||
|
LR Gapcloser Resource Report Resource Website 50+ mentions |
LR Gapcloser (RRID:SCR_016194) | alignment software, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies. | long, short, read, alignment, assembly, gap, closer, sequence, gene | PMID:30576505 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017021 | SCR_016194 | LR_Gapcloser | 2026-09-19 12:53:19 | 71 | ||||||||
|
L1000 Fireworks Display Resource Report Resource Website 10+ mentions |
L1000 Fireworks Display (RRID:SCR_016175) | L1000FWD | data processing software, data visualization software, software application, software resource, web application | Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase. | drug, small molecule, gene, expression, signature, moa, clinical, phase | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | PMID:29420694 | Freely available, Free, Available for download | SCR_016175 | L1000FWD: Large-scale Visualization of Drug-Induced Transcriptomic Signatures | 2026-09-19 12:53:18 | 16 | |||||||
|
LINCS Joint Project - Breast Cancer Network Browser Resource Report Resource Website 1+ mentions |
LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) | LJP-BCNB, LJP, BCNB | data access protocol, service resource, software resource, web service | Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations. | breast, cancer, tissue, cluster, drug, perturbation, cell, line, gene, expression |
is related to: L1000 Characteristic Direction Signature Search Engine is related to: LINCS Project |
Breast cancer | NCI U54 CA189201; NHGRI U54 HG006093; NHLBI U54 HL127365; NHLBI U54 HL127624 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | LINCS Joint Project, Breast Cancer Network Browser | 2026-09-19 12:53:19 | 1 | ||||
|
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 | 2026-09-19 12:53:22 | 1 | |||||||
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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 | 2026-09-19 12:53:21 | 10 | ||||||||||
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JAX Mice and Services Resource Report Resource Website 10+ mentions |
JAX Mice and Services (RRID:SCR_016408) | JAX, JAX MS, JMS, IMSR_JAX | biomaterial supply resource, material resource, organism supplier | Supplier of mice for research purposes. | RIN, Resource Information Network, mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model, RRID Community Authority |
is listed by: International Mouse Strain Resource is listed by: Resource Information Network is related to: Knockout Mouse Project Repository at JAX is parent organization of: Diversity Outbred Database works with: International Mouse Strain Resource |
SCR_016408 | Mice and Services, JAX Mice, JAX Mouse Service, JAX Mice Service, JAX Mouse and Services | 2026-09-19 12:53:22 | 14 | |||||||||
|
Shanghai Model Organisms Center Resource Report Resource Website 1+ mentions |
Shanghai Model Organisms Center (RRID:SCR_016407) | SMOC | biomaterial supply resource, commercial organization, material resource, organism supplier | Global biotechnology company based in Shanghai, China, specializing in custom model organisms, humanized and immunodeficient mice, and gene-editing services for preclinical research. Alternatively, in molecular biology, it can refer to knockout or mutant mice lacking the Smoc1 or Smoc2 genes (secreted modular calcium-binding proteins) used to study embryonic, eye, and limb development.Supplier of mice for research purposes. Provides technical services, model organisms, gene editing and decoding. | RIN, Resource Information Network, Shanghai Model Organisms Center Inc., mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model, RRID Community Authority |
is listed by: Resource Information Network works with: International Mouse Strain Resource |
http://www.shmo.com.cn/English/, https://www.modelorg.com/en/, https://www.modelorg.com/ | SCR_016407 | Shanghai Model Organisms Center, Inc. SMOCShanghai Model Organisms Center, Shanghai Model, Shanghai Model Center, Shanghai Model Organism Center | 2026-09-19 12:53:22 | 2 | ||||||||
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National Resource Center for Mutant Mice Resource Report Resource Website 1+ mentions |
National Resource Center for Mutant Mice (RRID:SCR_016406) | NRCMM, MARIP | biomaterial supply resource, material resource, organism supplier | Supplier of mice for research purposes. | mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model, transgenic | is listed by: International Mouse Strain Resource | SCR_016406 | National Resource Center for Mutant Mouse, Nanjing University Model Animal Research Institute, Model Animal Resource Information Platform, Model Animal Resource Imformation Platform | 2026-09-19 12:53:22 | 1 | |||||||||
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Taconic Biosciences Resource Report Resource Website 100+ mentions |
Taconic Biosciences (RRID:SCR_016410) | TAC, TB | biomaterial supply resource, material resource, organism supplier | Supplier of mice for research purposes. | RIN, Resource Information Network, mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model, transgenic, RRID Community Authority |
is listed by: Resource Information Network works with: International Mouse Strain Resource |
SCR_016410 | Taconic Mouse Supply, Taconic Mice, eTaconic, Taconic, Taconic Bioscience, Taconic Bio Sciences | 2026-09-19 12:53:22 | 232 |
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