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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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EyeBrowse Resource Report Resource Website 1+ mentions |
EyeBrowse (RRID:SCR_008000) | data set, data or information resource |
EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation. |
est, expressed sequence tag, eye, gene, genome, cataract, cdna, chicken, clone, cluster, cornea, cornea disease, cow, data, disease, dog, human, locus, maturation, mouse, myopia, photoreceptor, rat, retina, rhesus, rna polymerase-ii, tag, zebrafish, data analysis software, eye tracking device |
is listed by: 3DVC has parent organization: University of California at Santa Cruz; California; USA |
Retinal disease, Cataract, Myopia, Cornea disease | NEIBank | nif-0000-07733 | SCR_008000 | EyeBrowse | 2026-08-06 09:27:03 | 3 | |||||||
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CistromeFinder Resource Report Resource Website 1+ mentions |
CistromeFinder (RRID:SCR_005405) | CistromeFinder | data set, data or information resource | Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update. | chip-seq, dnase-seq, cell, tissue, disease, histone modification, transcription factor, chromatin regulator, dnase, binding site, gene, transcription regulation |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: CistromeMap has parent organization: Dana-Farber Cancer Institute |
PMID:23508969 | The community can contribute to this resource | OMICS_00528 | SCR_005405 | 2026-08-06 09:26:20 | 2 | |||||||
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Cardiovascular Gene Ontology Annotation Initiative Resource Report Resource Website 1+ mentions |
Cardiovascular Gene Ontology Annotation Initiative (RRID:SCR_004795) | CV-GO, BHF-UCL | data set, data or information resource | Full Gene Ontology annotation to genes associated with cardiovascular processes. Every GO annotation made, is attributed to an identified source, such as a publication identifier (PMID), and an indication of the type of evidence which supports the association between the gene product and the GO term. Over 4,000 cardiovascular associated genes have been identified. A variety of tools have been provided to enable cardiovascular scientists to review the annotation of their ''''favorite'''' gene and suggest information that may be missing, inaccurate or incomplete in these annotations. Annotation suggestions can be sent through the feedback form or by email. The Gene Ontology (GO) vocabulary is the established standard for the functional annotation of gene products. By using GO to curate scientific literature and by integrating results from high-quality high-throughput experiments they will create an information-rich resource for the cardiovascular-research community, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research. | cardiovascular process, heart disease, cardiovascular, heart, cardiovascular system, annotation, gene, functional annotation, gene product, gold standard |
is related to: Gene Ontology is related to: IntAct has parent organization: University College London; London; United Kingdom |
British Heart Foundation SP/07/007/23671 | PMID:21419760 PMID:19046747 |
The community can contribute to this resource | nlx_79058 | http://www.ebi.ac.uk/GOA/CVI/ | SCR_004795 | Cardiovascular Gene Ontology, Cardiovascular GO Annotation Initiative | 2026-08-06 09:26:14 | 2 | ||||
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Target genes of Wnt/beta-catenin signaling Resource Report Resource Website 10+ mentions |
Target genes of Wnt/beta-catenin signaling (RRID:SCR_007022) | Target genes of Wnt/beta-catenin signaling | data set, data or information resource | A list of target genes of Wnt/beta-catenin signaling. Suggestions for additions are welcome. Direct targets are defined as those with Tcf binding sites and demonstrating that these sites are important. | target gene, wnt/beta-catenin signaling, wnt, beta-catenin, signaling, gene | has parent organization: Stanford University; Stanford; California | Colon cancer, Tumor, Adenocarcinoma, Melanoma, Cancer | The community can contribute to this resource | nlx_156867 | SCR_007022 | 2026-08-06 09:26:46 | 24 | |||||||
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In-Vivo Cellular and Molecular Imaging Center, Brussels Resource Report Resource Website |
In-Vivo Cellular and Molecular Imaging Center, Brussels (RRID:SCR_008047) | service resource, core facility, access service resource | Imaging core offering multiple small animal imaging modalities including MicroSPECT, Optical imaging, MicroCT and Ultrasound have been centralized together with a unit for probe development and a vivarium for the housing of animals in one laboratory. | echography, expression, fluorescence, gene, animal, bioluminescence, bli, cellular, computed tomography, development, disease, imaging, interaction, in vivo, living, magnetic resonance imaging, microct, microspect, molecular, optical, pathogenesis, positron emission tomography (pet), probe, resolution, single photon emission computed tomography, therapeutic, ultrasound | has parent organization: Vrije Universiteit Brussel; Brussels; Belgium | nif-0000-10270 | SCR_008047 | VUB ICMIC | 2026-08-06 09:27:04 | 0 | |||||||||
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University at Albany Center for Functional Genomics DNA Microarray Core Facility Resource Report Resource Website |
University at Albany Center for Functional Genomics DNA Microarray Core Facility (RRID:SCR_012502) | UAlbany CFG DNA Microarray Core Facility | service resource, core facility, access service resource | Core provides microarray services for Affymetrix GeneChip arrays, Agilent microarrays, NimbleGen microarrays and custom-produced spotted cDNA microarrays. Projects developed through DNA Microarray Center have made use of arrays from variety of genomes, eukaryotic, prokaryotic, and plant. Core services includes RNA/DNA isolation, gene expression, miRNA, Chip-chip, Rip-chip and DNA methylation services. Provides bioinformatics tools for further analysis of results of expression experiments. | DNA, microarray, functional, genomics, RNA, isolation, gene, expression, Chip-chip, Rip-chip, methylation, experiment, analysis |
is listed by: ScienceExchange has parent organization: University at Albany Center for Functional Genomics |
Restricted | SciEx_30 | SCR_012502 | CFG, University at Albany DNA Microarray Core Facility, University at Albany, UAlbany, Functional Genomics, Center for Functional Genomics, DNA Microarray | 2026-08-06 09:27:55 | 0 | |||||||
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Salk Institute Functional Genomics Core Facility Resource Report Resource Website |
Salk Institute Functional Genomics Core Facility (RRID:SCR_014841) | FGL | service resource, core facility, access service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5,2024.Core facility that provides Salk researchers access to gene expression analysis services such as whole-genome expression and genotyping using Affymetrix GeneChip technology, high-throughput qPCR and SNP services using Fluidigm Biomark System and Applied Biosystems 7900HT System, and DNA miniprep extraction using Qiagen BioRobot. | core facility, la jolla, genomics, gene, snp, genotype | Salk Institute Functional Genomics Core Facility ; NCI CCSG P30 014195 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_014841 | 2026-08-06 09:28:28 | 0 | |||||||||
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scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, software application, software resource, data processing software | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-08-06 09:28:56 | 92 | ||||
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Bulked segregation analysis tools for outbreeding species Resource Report Resource Website 1+ mentions |
Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) | BSATOS | time-series analysis software, software resource, 1d time-series analysis software, data analysis software, data processing software, software application | Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data. | next, generation, sequencing, bulked, segregation, analysis, outbreeting, specie, gene, mapping, data | Free, Available for download, Freely available | SCR_017009 | Bulked segregation analysis tools for outbreeding species, Bulked Segregation Analysis Tools for Outbreeding Species, BSATOS | 2026-08-06 09:28:59 | 2 | |||||||||
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Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | portal, project portal, data or information resource, atlas | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-08-06 09:28:57 | 195 | ||||||||
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cd-CAP software Resource Report Resource Website 1+ mentions |
cd-CAP software (RRID:SCR_016843) | software resource, network analysis software, data analysis software, data processing software, software application | Software designed for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. | simultaneous, detection, connected, subnetwork, interaction, network, gene, exhibit, conserved, alteration, pattern, tumor, sample | Free, Available for download, Freely available | SCR_016843 | 2026-08-06 09:28:57 | 1 | |||||||||||
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NetworkAnalyst Resource Report Resource Website 500+ mentions |
NetworkAnalyst (RRID:SCR_016909) | software resource, network analysis software, service resource, data access protocol, production service resource, data analysis software, data analysis service, web service, data processing software, software application, analysis service resource | Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data. | gene, expression, profiling, meta, data, analysis, statistical, visual, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25950236 | Free, Freely available, Tutorial available | biotools:networkanalyst | https://bio.tools/networkanalyst | SCR_016909 | 2026-08-06 09:28:58 | 635 | |||||||
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VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | data analysis software, software application, software resource, data processing software | Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections. | variant, antigen, profiling, data, genome, transcriptome, proteome, gene, expression, infection, Trypanosoma, bio.tools |
is listed by: Debian is listed by: bio.tools requires: Python Programming Language |
Free, Available for download, Freely available | biotools:VAPPER | https://bio.tools/VAPPER | SCR_016993 | VAP, VariantAntigenProfilingPER | 2026-08-06 09:28:59 | 1 | ||||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data analysis software, software application, software resource, data processing software | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | NIDDK R24 DK096518; NHLBI R24 HL123482; NIDDK R01 DK115791; Fraternal Order of Eagles Diabetes Research Center ; University of Iowa Center for Gene Therapy ; Carver Chair in Molecular Medicine ; NIGMS T32 GM082729 |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-08-06 09:28:59 | 5 | |||||||||
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Java Treeview Resource Report Resource Website 50+ mentions |
Java Treeview (RRID:SCR_016916) | TreeView | data visualization software, software application, software resource, data processing software | Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure. | gene, expression, data, visualization, microarray, interactive, display, cluster, dataset |
is related to: University of Hamburg; Hamburg; Germany has parent organization: Princeton University; New Jersey; USA |
Free, Available for download, Freely available | https://bitbucket.org/TreeView3Dev/treeview3/ | SCR_016916 | TreeView3, Treeview, Java TreeView | 2026-08-06 09:28:55 | 52 | |||||||
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sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | data analysis software, software application, software resource, data processing software | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NIDDK R01 DK094699; NHGRI R01 HG006129 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth, https://bio.tools/sleuth, https://bio.tools/sleuth | SCR_016883 | 2026-08-06 09:28:58 | 24 | ||||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 1+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | project portal, data or information resource, portal, catalog, database | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIH ; NIDDK |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-08-06 09:28:58 | 9 | ||||||||
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XL-mHG Resource Report Resource Website |
XL-mHG (RRID:SCR_016846) | xlmhg | data analysis software, software application, software resource, data processing software | Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment. | semiparametric, test, enrichment, ranked, list, gene, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:XL-mHG, biotools:XL-mHG | https://bio.tools/XL-mHG, https://bio.tools/XL-mHG, https://bio.tools/XL-mHG | SCR_016846 | xlminimumhypergeometric, XL-minimum HyperGeometric test, XL-minimum HyperGeometric, xlmhg, XL-mHG | 2026-08-06 09:28:54 | 0 | ||||||
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TranscriptAchilles Resource Report Resource Website 1+ mentions |
TranscriptAchilles (RRID:SCR_016849) | TranscriptAchilles | sequence analysis software, software resource, data analysis software, data processing software, web application, software application | Software genome-wide tool to predict transcript biomarkers of gene essentiality in cancer. This tool can be used to predict new potential target genes with their corresponding biomarkers (either transcript or gene expression). | predict, transcript, biomarker, gene, inhibition, isoform, cancer, cell line, expression, essentiality, target gene | Free, Available for download, Freely available | https://gitlab.com/fcarazo.m/transcriptachilles/ | SCR_016849 | 2026-08-06 09:28:58 | 1 | |||||||||
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Tunable Biclustering Algorithm Resource Report Resource Website 1+ mentions |
Tunable Biclustering Algorithm (RRID:SCR_017121) | TuBA | data analysis software, software application, software resource, data processing software | Software tool as graph based unsupervised biclustering algorithm to identify alterations in tumors based on hypothesis that gene pairs relevant to clinical process share statistically significant number of samples with extreme expression. | graph, unsupervised, algorithm, identify, alteration, tumor, gene, pair, significant, expression | has parent organization: Rutgers University; New Jersey; USA | Free, Available for download, Freely available | SCR_017121 | 2026-08-06 09:28:59 | 2 |
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