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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-19 12:53:43 | 6 | ||||||
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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 | 2026-09-19 12:53:41 | 10 | |||||||||
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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 | 2026-09-19 12:53:41 | 5 | ||||||||||
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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 | 2026-09-19 12:53:41 | 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 | 2026-09-19 12:53:42 | 3 | |||||||||
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scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
Cancer Research UK A17197; European Molecular Biology Laboratory ; National Health and Medical Research Council of Australia APP1112681; Oxford Single Cell Biology Consortium ; United Kingdom Medical Research Council |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-09-19 12:53:15 | 187 | ||||||
|
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 | 2026-09-19 12:53:19 | 1 | ||||||||
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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 | 2026-09-19 12:53:18 | 135 | |||||||||
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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 | 2026-09-19 12:53:18 | 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 | 2026-09-19 12:53:18 | 364 | |||||||||
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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 | 2026-09-19 12:53:19 | 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 | 2026-09-19 12:53:19 | 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 | 2026-09-19 12:53:22 | 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 | 2026-09-19 12:53:20 | 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 | 2026-09-19 12:53:20 | 0 | |||||||||
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National Applied Research Laboratories Resource Report Resource Website 1+ mentions |
National Applied Research Laboratories (RRID:SCR_016405) | NLAC, RMRC-NLAC, NARL, RMRC NARL, RMRC NLAC, NLAC RMRC | 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_016405 | National Laboratory Resource Center, National Laboratory Resource Center Rodent Model Resource Center, National Applied Research Laboratory, Rodent Model Resource Center | 2026-09-19 12:53:22 | 2 | |||||||||
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Oak Ridge Collection at JAX Resource Report Resource Website |
Oak Ridge Collection at JAX (RRID:SCR_016409) | ORNL, ORC | 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 | is listed by: International Mouse Strain Resource | SCR_016409 | Oak Ridge Collection, Oak Ridge Laboratory, JAX Oak Ridge, Oak Ridge Lab, Oakridge, The Oak Ridge National Laboratory (ORNL), Oak Ridge National Laboratory, Oak Ridge | 2026-09-19 12:53:22 | 0 | |||||||||
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Oriental BioService Inc. Resource Report Resource Website 1+ mentions |
Oriental BioService Inc. (RRID:SCR_016404) | OBS | 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_016404 | Oriental BioService, Oriental BioServices | 2026-09-19 12:53:22 | 8 | |||||||||
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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 | 2026-09-19 12:53:21 | 227 | ||||||||
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GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | data analysis software, data processing software, software application, software resource | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | 2026-09-19 12:53:25 | 76 |
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