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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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USP Molecular Genetics and Bioinformatics Laboratory Resource Report Resource Website 1+ mentions |
USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) | USP Molecular Genetics and Bioinformatics Laboratory | data or information resource, laboratory portal, organization portal, portal | Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory. | genetics, bioinformatics, data mining, genome, gene | has parent organization: University of Sao Paulo; Sao Paulo; Brazil | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149158 | SCR_000605 | University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory, USP Laboratorio de Genetica Molecular e Bioinformatica, University of Sao Paulo Molecular Genetics and Bioinformatics Laboratory, USP Molecular Genetics Bioinformatics Laboratory, USP Molecular Genetics and Bioinformatic Laboratory | 2026-08-29 11:20:32 | 1 | |||||||
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Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | data processing software, software application, software resource, workflow software | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Key Research and Development Program 2017YFC0908500 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 81573023 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-08-29 11:26:04 | 2 | |||||
|
Track-A-Worm Resource Report Resource Website 1+ mentions |
Track-A-Worm (RRID:SCR_018299) | data analysis software, data processing software, software application, software resource | Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification. | Quantitative assessment, C.Elegans locomotory, bending behavior, behavioral analysis, gene, moving worm position, body shape, automated recording | is related to: University of Connecticut; Connecticut; USA | NIGMS R01 GM083049; NIMH R01 MH085927 |
PMID:23922769 | Free, Available for download, Freely available | SCR_018299 | Tracker-A-Worm version 1.0, Tracker-A-Worm version 2.0 | 2026-08-29 11:26:06 | 4 | |||||||
|
Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | data access protocol, data or information resource, database, software resource, web service | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. | Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis | has parent organization: La Jolla Institute for Immunology | NCRR S10 RR027366; NIAID R24 AI108564; NIH Office of the Director S10 OD016262; William K. Bowes Jr Foundation |
PMID:30449622 | Free, Freely available | SCR_018259 | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics | 2026-08-29 11:26:06 | 73 | ||||||
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Codon Usage Analyzer Resource Report Resource Website |
Codon Usage Analyzer (RRID:SCR_018500) | Bio::CUA, Bio-CUA | data analysis software, data processing software, software application, software resource | Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems. | Codon usage analyzer, codon, codon usage bias, genome, gene, codon, sequence | has parent organization: University of Rochester; New York; USA | David and Lucile Packard Foundation ; University of Rochester |
DOI:10.1101/022814 | Free, Freely available | https://metacpan.org/release/Bio-CUA | SCR_018500 | 2026-08-29 11:26:08 | 0 | ||||||
|
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 | 2026-08-29 11:26:11 | 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 | 2026-08-29 11:25:50 | 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 | 2026-08-29 11:26:15 | 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 | 2026-08-29 11:25:55 | 7 | |||||||
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miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | data access protocol, data or information resource, database, software resource, web service | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-08-29 11:25:37 | 73 | ||||||
|
SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | analysis service resource, controlled vocabulary, data analysis service, data or information resource, ontology, production service resource, service resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | CERCA Program/Generalitat de Catalunya ; European Union ; German Federal Ministry of Education and Research ; NINDS NS36251; Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-08-29 11:25:35 | 187 | |||||||
|
3D Genome Resource Report Resource Website 10+ mentions |
3D Genome (RRID:SCR_017525) | service resource | Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | 3D, genome, organization, gene, regulation, data, visualization, chromatin, interaction, omic, ChIPseq, RNAseq, regulatory, structure |
is related to: Encode has parent organization: Pennsylvania State University |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017525 | 2026-08-29 11:26:00 | 20 | ||||||||||
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MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/, https://bio.tools/MCScan | SCR_017650 | Multiple Collinearity Scan | 2026-08-29 11:25:47 | 42 | |||||||
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shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | analysis service resource, production service resource, service resource, software resource, web application | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo | SCR_017605 | 2026-08-29 11:25:46 | 0 | ||||||
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Single Cell Developmental Database Resource Report Resource Website 1+ mentions |
Single Cell Developmental Database (RRID:SCR_017546) | SCDevDB | data or information resource, data repository, data set, database, service resource, storage service resource | Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes. | Single, cell, gene, expression, profile, human, development, process, data | GRF Research Project ; RGC General Research Fund |
DOI:10.3389/fgene.2019.00903 | Free, Available for download, Freely available | SCR_017546 | Single-Cell Developmental Database | 2026-08-29 11:25:43 | 2 | |||||||
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Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | 2026-08-29 11:25:43 | 0 | |||||||||||
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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 | 2026-08-29 11:25:15 | 18 | ||||||||||||
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findMotif.pl Resource Report Resource Website 1+ mentions |
findMotif.pl (RRID:SCR_016417) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software tool to analyze the promoters of genes and look for motifs that are enriched in the target gene promoters relative to other promoters. Used for gene based analysis to provide a list of genes that should contain the same elements, such as genes that are co-regulated. It includes gene ontology analysis and can be used to look for RNA motifs in mRNAs. | analyze, promoter, gene, motif, target, relative, same, element, ontology, RNA, mRNA |
is related to: HOMER has parent organization: University of California at San Diego; California; USA |
Free, Available for download, Freely available | SCR_016417 | 2026-08-29 11:25:43 | 4 | ||||||||||
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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 | 2026-08-29 11:25:18 | 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 | 2026-08-29 11:25:18 | 1 |
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