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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Zebrafish RNAi Database Resource Report Resource Website |
Zebrafish RNAi Database (RRID:SCR_008965) | Zebrafish RNAi Database | storage service resource, topical portal, service resource, organism-related portal, data repository, data or information resource, portal | Community built zebrafish RNAi platform that contains plasmids, successfully targeted genes and shRNA sequences, and a forum for discussion. This is a true community platform with users who add data, modify entiries, request features and share using the discussion board. | plasmid, gene, shrna sequence, rnai, method | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | nlx_152032 | SCR_008965 | 2026-08-06 09:27:15 | 0 | |||||||||
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Molecular Libraries Program Resource Report Resource Website 10+ mentions |
Molecular Libraries Program (RRID:SCR_008847) | MLP | topical portal, service resource, production service resource, material analysis service, data or information resource, organization portal, portal, analysis service resource | High throughput screening services to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways, along with medicinal chemistry and informatics. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. The NIH Molecular Libraries Initiative NIH is designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. As these HTS Technologies were not previously available to the public sector, many investigators may not be familiar with the components and requirements of high throughput screening. A key challenge is to identify small molecules effective at modulating a given biological process or disease state. The Molecular Libraries Roadmap, through one of its components, the Molecular Libraries Probe Production Centers Network (MLPCN), offers biomedical researchers access to the large-scale screening capacity, along with medicinal chemistry and informatics necessary to identify chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. There are two kinds of data that are available to the scientific community through a dedicated database: Chemical Compounds and Bioassay Results (NCBI). Various types of data, including informative records on substances, compound structures, and biologically active properties of small molecules are housed respectively within PubChem''''s three primary databases: PCSubstance, PCCompound, and PCBioAssay. To date, PubChem contains over 11 million substance records, details about approximately 5.5 million unique compound structures with links to bioassay descriptions, relevant literature, references, and assay data points and over 250 bioassays, a good percentage of which were contributed by the pilot phase of the MLP. The deposition will continue during the current MLPCN phase. NIH anticipates that these projects will also facilitate the development of new drugs, by providing early stage chemical compounds that will enable researchers in the public and private sectors to validate new drug targets, which could then move into the drug-development pipeline. This is particularly true for rare diseases, which may not be attractive for development by the private sector. Funding opportunities are available through the site. | molecule, compound, probe, small molecule, high throughput screening, gene, cell, biochemical pathway, drug development, protein, pathway |
is used by: LINCS Information Framework is related to: BARD is related to: NIH Clinical Collection is related to: PubChem has parent organization: National Institutes of Health |
NIH | nlx_146246 | SCR_008847 | Molecular Libraries, Molecular Libraries Initiative | 2026-08-06 09:27:13 | 15 | |||||||
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Human Variation DB Resource Report Resource Website |
Human Variation DB (RRID:SCR_009014) | Human Variation DB | storage service resource, service resource, data repository, data or information resource, database | A repository database to achieve continuous and intensive management of GWAS data and variation data identified by next generation sequencing (NGS) and data-sharing among researchers. In this database, variations including short/long insertions / deletions and structural variations related to disease susceptibility, virus resistance, and drug response are registered along with statistical genetic results and simple clinical characteristics to clarify the locus specific characteristics. Currently this database contains information extracted from scientific papers and next generation sequencing results and other small scale experimental results of several research laboratories. Mutation data submission is greatly appreciated. | gene, genome, disease, snp, next generation sequencing, gwas, genetic variation, mutation, copy number variation, insertion, deletion, structural variation | has parent organization: NBDC - National Bioscience Database Center | Japan Science and Technology Agency | PMID:19629137 PMID:21385384 |
The community can contribute to this resource | nlx_153886 | SCR_009014 | Human Genome Variation Database | 2026-08-06 09:27:18 | 0 | |||||
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CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | data analysis software, software application, software resource, data processing software | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-08-06 09:27:15 | 413 | ||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | data analysis software, software application, software resource, data processing software | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-08-06 09:27:13 | 8 | |||||
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AgingDB Resource Report Resource Website |
AgingDB (RRID:SCR_010226) | AgingDB | storage service resource, service resource, data repository, data or information resource, database | A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments. | oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factor |
is related to: Gene Ontology has parent organization: Pusan National University; Busan; South Korea |
Aging | PMID:23604914 | The community can contribute to this resource | nlx_156773 | http://aging.pharm.pusan.ac.kr/AgingDB/ | SCR_010226 | Aging Database, Aging DB | 2026-08-06 09:27:32 | 0 | ||||
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miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | Helmholtz-Alliance on Systems Biology ; Helmholtz Association ; German Ministry of Education and Research ; Senate of Berlin ; China Scholarship Council ; Max Delbrück Centrum Systems Biology Network |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-08-06 09:27:44 | 163 | |||||
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Evex Resource Report Resource Website 10+ mentions |
Evex (RRID:SCR_010509) | software resource, text-mining software, data or information resource, software application, database | EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. | gene, protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium |
biotools:evex, nlx_158731 | https://bio.tools/evex | SCR_010509 | 2026-08-06 09:27:35 | 18 | |||||||||
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Gene Regulation Ontology Resource Report Resource Website |
Gene Regulation Ontology (RRID:SCR_010590) | GRO, BOOTStrep | controlled vocabulary, ontology, data or information resource | Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). | owl, genomic, proteomic, biological process, gene regulation, gene expression, gene, transcription factor, process, molecule, biological_process |
is listed by: BioPortal is listed by: OBO has parent organization: European Bioinformatics Institute |
nlx_157415, nlx_46399 | http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html, http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest | SCR_010590 | Gene Regulation Ontology - Ontological resource from the BOOTStrep project for the representation of gene regulation events | 2026-08-06 09:27:37 | 0 | |||||||
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Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | software resource, service resource, production service resource, data analysis service, analysis service resource | A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. | microbial, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Glimmer-MG is related to: GlimmerHMM has parent organization: Johns Hopkins University; Maryland; USA |
DOI:10.1093/nar/26.2.544 | Open unspecified license, OSI certified | OMICS_01486, biotools:glimmer | https://bio.tools/glimmer, https://sources.debian.org/src/tigr-glimmer/ | SCR_011931 | Glimmer - Microbial Gene-Finding System | 2026-08-06 09:27:48 | 637 | |||||
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CummeRbund Resource Report Resource Website 100+ mentions |
CummeRbund (RRID:SCR_014568) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions. | r software, cufflink, rna-seq, sqlite, gene, transcript, transcription start site, cds region, r, rnaseq, rna seq, bio.tools, FASEB list |
uses: R Project for Statistical Computing is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard University; Cambridge; United States |
Free, Freely available | biotools:cummerbund, OMICS_07349 | https://bio.tools/cummerbund, https://sources.debian.org/src/r-bioc-cummerbund/ | SCR_014568 | 2026-08-06 09:28:21 | 361 | ||||||||
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scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, data visualization software, software application | 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 |
National Health and Medical Research Council of Australia APP1112681; European Molecular Biology Laboratory ; Cancer Research UK A17197; United Kingdom Medical Research Council ; Oxford Single Cell Biology Consortium |
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) | 2026-08-06 09:28:47 | 173 | ||||||
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HumanNet Resource Report Resource Website 100+ mentions |
HumanNet (RRID:SCR_016146) | software resource, data analysis software, data or information resource, data processing software, web application, software application, database | 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 |
National Research Foundation of Korea (NRF) ; Korean government (MEST) 2010-0017649; POSCO TJ ; U.S. Army Research 58343-MA; Welch F1515; Packard Foundations ; Wellcome Trust 076113; Wellcome Trust 085475 |
Freely available | SCR_016146 | 2026-08-06 09:28:46 | 132 | |||||||||
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Clinker Resource Report Resource Website 100+ mentions |
Clinker (RRID:SCR_016140) | data visualization software, software application, software resource, data processing software | 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 | 2026-08-06 09:28:48 | 286 | |||||||||
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AIIA-GMT Resource Report Resource Website |
AIIA-GMT (RRID:SCR_016397) | software application, data access protocol, web service, software resource | 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 | 2026-08-06 09:28:51 | 0 | |||||||||||
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Phenocarta Resource Report Resource Website 1+ mentions |
Phenocarta (RRID:SCR_016273) | software resource, data analysis software, data or information resource, data processing software, software application, database | 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 | 2026-08-06 09:28:53 | 2 | |||||||
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AspireDB Resource Report Resource Website |
AspireDB (RRID:SCR_016272) | software resource, data analysis software, data processing software, web application, software 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 | Canadian Foundation for Innovation ; BC Knowledge Development Fund |
Account required, Freely available | https://github.com/ppavlidis/aspiredb, http://pavlab.msl.ubc.ca/software-and-resources/ | SCR_016272 | 2026-08-06 09:28:47 | 0 | |||||||||
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SL-quant Resource Report Resource Website 1+ mentions |
SL-quant (RRID:SCR_016205) | SLQ | sequence analysis software, software resource, data analysis software, data processing software, software application | 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 | 2026-08-06 09:28:52 | 1 | ||||||||
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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 set, software resource, data access protocol, service resource, web service, data or information resource, database | 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 |
NHLBI U54 HL127624; NCI U54 CA189201 |
PMID:28413689 | Free, Freely available | SCR_016177 | 2026-08-06 09:28:49 | 8 | |||||||
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Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | software resource, web application, data or information resource, data processing software, data visualization software, software application, database | 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 ; NIGMS R01 GM098316; NHLBI U54 HL127624; NCI U54 CA189201 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-08-06 09:28:51 | 127 |
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