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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Tests for deviation from Hardy-Weinberg equilibrium Resource Report Resource Website 10+ mentions |
Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) | data analysis software, data processing software, software application, software resource | Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases. | deviation, Hardy-Weinberg, equilibrium, test, association, population, genetic, identify, susceptibility, gene, disease, single, nucleotide, polymorphisms, snp, allele | SCR_016496 | 2026-09-12 12:58:40 | 18 | ||||||||||||
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Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | data access protocol, service resource, software resource, web service | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NCI U24 CA224260; NHLBI U54 HL127624 |
PMID:30169739 | Restricted | SCR_016489 | Drug Gene Budger | 2026-09-12 12:58:40 | 0 | ||||||
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Thermo Fisher: GeneChip� Scanner 3000 7G Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk, https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-09-12 12:58:40 | 1 | |||||||||
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SABRe CVD Initiative Resource Report Resource Website |
SABRe CVD Initiative (RRID:SCR_016572) | SABRe CVD | data or information resource, disease-related portal, portal, topical portal | Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation. | generate, biomarker, discovery, data, Framingham, Heart, Study, gene, expression, omicdata | cardiovascular disease, atherosclerosis | Free, Partially available for public, Requested authorized access | SCR_016572 | Systems Approach to Biomarker Research in CardioVascular Disease | 2026-09-12 12:58:41 | 0 | ||||||||
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MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome BC ; Genome Canada |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-09-12 12:58:40 | 15 | ||||||
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NanoAmpli-Seq Resource Report Resource Website 1+ mentions |
NanoAmpli-Seq (RRID:SCR_016710) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing. | amplicon, sequencing, 16S rRNA, mixed, microbial, communities, nanopore, platform, gene |
is related to: INC-Seq has parent organization: University of Glasgow; Glasgow; United Kingdom |
EPSRC EP/M016811/1; NERC NE/L011956/1 |
DOI:10.1101/244517 | Free, Available for download, Freely available | https://www.protocols.io/view/nanoampli-seq-bioinformatics-workflow-u25eyg6 | SCR_016710 | 2026-09-12 12:58:43 | 1 | |||||||
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Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-09-12 12:58:42 | 0 | |||||||
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dCAS Resource Report Resource Website |
dCAS (RRID:SCR_016612) | dCAS | software resource, web application | Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene | is listed by: NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016612 | Desktop cDNA Annotation System | 2026-09-12 12:58:42 | 0 | ||||||||
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EPIGEN Resource Report Resource Website 10+ mentions |
EPIGEN (RRID:SCR_000093) | EPIGEN | consortium, data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | epilepsy, genetics, gene, mri, genetic variation, clinical |
has parent organization: Duke University; North Carolina; USA has parent organization: University College London; London; United Kingdom has parent organization: Beaumont Hospital; Dublin; Ireland has parent organization: Royal College of Surgeons in Ireland; Dublin; Ireland has parent organization: Free University of Brussels; Brussels; Belgium |
Epilepsy | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143740 | SCR_000093 | EPIGEN: An international consortium dedicated to tackling epilepsy through genetics, EPIGEN Consortium | 2026-09-12 12:55:03 | 24 | ||||||
|
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 | 2026-09-12 12:59:04 | 0 | |||||
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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 | 2026-09-12 12:59:04 | 34 | ||||||
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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 | 2026-09-12 12:59:07 | 0 | ||||||||
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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 | 2026-09-12 12:59:08 | 7 | |||||||
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clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
2007 Chang-Jiang Scholars Program ; Fundamental Research Funds for the Central Universities ; Guangdong Natural Science Research Grant ; National 973 Projects of China ; National Natural Science Foundation of China |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler, https://guangchuangyu.github.io/software/clusterProfiler/, https://bio.tools/clusterprofiler | SCR_016884 | Cluster Profiler | 2026-09-12 12:58:45 | 13465 | |||||
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PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | simulation software, software application, software resource | Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | ARO W911NF1110473; Canada Research Chairs program ; Canadian Institutes of Health Research ; Crohn’s and Colitis Foundation of America ; Howard Hughes Medical Institute ; NHGRI R01 HG004872; NHGRI R01 HG005969; NHGRI U01 HG004866; NIDDK P01 DK078669; NSF CAREER DBI1053486; Sloan Foundation |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-09-12 12:58:45 | 45 | |||||
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Stemformatics Resource Report Resource Website 1+ mentions |
Stemformatics (RRID:SCR_017002) | data or information resource, data set, organization portal, portal, service resource | Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. | gene, expression, data, stem, cell, community, microarray, RNA, sequencing, dataset, cluster | ARC Discovery Project ; ARC Future Fellowship ; ARC Special Research Initiative to Stem Cells Australia ; JEM Research Foundation philanthropic funding ; QLD Government Smart Futures Fellowship ; University of Melbourne Centre for Stem Cell Systems |
PMID:23466562 | Free, Available for download, Freely available | SCR_017002 | 2026-09-12 12:58:47 | 1 | |||||||||
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Haystack Resource Report Resource Website 1+ mentions |
Haystack (RRID:SCR_017087) | data analysis software, data processing software, software application, software resource, software toolkit | Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline. | epigenetic, variability, cell, plasticity, chromatin, transcription, factor, motif, structure, gene, regulation, analysis |
is related to: Python Programming Language has parent organization: Harvard University; Cambridge; Massachusetts |
Free, Available for download, Freely available | https://github.com/pinellolab/haystack_bio | SCR_017087 | haystack, haystack_bio | 2026-09-12 12:58:48 | 3 | ||||||||
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dndSCV Resource Report Resource Website 10+ mentions |
dndSCV (RRID:SCR_017093) | data analysis software, data processing software, software application, software resource | Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets. | dN/dS, method, quantify, selection, cancer, somatic, evolution, missense, nonsense, essential, splice, mutation, gene, genome, dataset |
uses: devtools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017093 | 2026-09-12 12:58:48 | 36 | ||||||||||
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GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | data analysis software, data processing software, software application, software resource | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-09-12 12:58:48 | 53 | |||||||||
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RNAmmer Resource Report Resource Website 100+ mentions |
RNAmmer (RRID:SCR_017075) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, standalone software, web service | Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. | predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA | has parent organization: Technical University of Denmark; Lyngby; Denmark | Danish Center for Scientific Computing ; EMBIO at the University of Oslo ; European Union ; Research Council of Norway |
PMID:17452365 | Restricted | SCR_017075 | 2026-09-12 12:58:48 | 120 |
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