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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | SciCrunch Registry | 2026-09-19 12:58:15 | 1908 | ||||||
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Mutant Mouse Resource and Research Center - Jackson Laboratory Resource Report Resource Website 10+ mentions |
Mutant Mouse Resource and Research Center - Jackson Laboratory (RRID:SCR_016446) | MMRRC JAX, JAX MMRRC, JAX MMR | biomaterial supply resource, material resource | Center for mutant mouse research and distribution. The objectives of the JAX MMRRC are to: identify and evaluate biomedically-significant mice, import/acquire and archive mouse strains, distribute mouse strains, and operate a control program to ensure genetic stability. | mouse, mutation, clinical, research, biomedicine, genetics, gene, strain | is organization facet of: Mutant Mouse Resource and Research Center | NIH Office of the Director U42 OD010921 | SCR_016446 | SciCrunch Registry | JAX Mutant Mouse Resource and Research Center, Mutant Mouse Resource and Research Center - JAX, Jackson Laboratory MMRRC, Jackson Laboratory Mutant Mouse Resource and Research Center | 2026-09-19 12:58:15 | 23 | ||||||||
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CAGE Basic Viewer for Mus musculus Resource Report Resource Website 1+ mentions |
CAGE Basic Viewer for Mus musculus (RRID:SCR_000451) | CAGE Basic Viewer | data or information resource, data set | A web system, which could search and display to current CAGE library information in CAGE Database. | genome, gene, tissue, library, map, clone, cage, tag, mus musculus, primer, cdna, transcription, mouse development, theiler stage |
is related to: Functional Annotation of the Mammalian Genome is related to: CAGE has parent organization: RIKEN |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30231 | SCR_000451 | SciCrunch Registry | 2026-09-19 12:58:30 | 1 | ||||||||
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GeneWays Resource Report Resource Website |
GeneWays (RRID:SCR_000572) | Geneways | service resource | System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information. | pathway, molecule, literature, natural language processing, gene, protein, interaction, database |
is listed by: OMICtools has parent organization: Argonne National Laboratory has parent organization: Columbia University; New York; USA |
DOE ; NIGMS GM61372; NSF |
PMID:15016385 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30019, SCR_008368, OMICS_01182 | http://anya.igsb.anl.gov/genewaysApp | SCR_000572 | SciCrunch Registry | GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data, GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data | 2026-09-19 12:58:30 | 0 | ||||
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GlimmerHMM Resource Report Resource Website 500+ mentions |
GlimmerHMM (RRID:SCR_002654) | GlimmerHMM | software resource, source code | A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). | gene, hidden markov model |
is related to: Glimmer has parent organization: Johns Hopkins University; Maryland; USA |
NIH ; NLM R01-LM06845; NLM R01-LM007938 |
PMID:15145805 | Free, Available for download, Freely available | nlx_156092 | SCR_002654 | SciCrunch Registry | GlimmerHMM - Eukaryotic Gene-Finding System | 2026-09-19 12:58:34 | 643 | |||||
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ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | SciCrunch Registry | 2026-09-19 12:58:33 | 35 | ||||||
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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 or information resource, data set | 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 | SciCrunch Registry | Cardiovascular Gene Ontology, Cardiovascular GO Annotation Initiative | 2026-09-19 12:58:37 | 2 | ||||
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Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes Resource Report Resource Website 1+ mentions |
Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) | data or information resource, data set | Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. | molecular, taxonomy, lung, carcinoma, cancer, death, mrna, expression, sequence, data, adenocarcinoma, neuroendocrine, gene, type ii pneumocyte, analysis, metastasis, integration, mrna expression profiling | has parent organization: Broad Institute | Lung cancer | NCI U01 CA84995 | PMID:11707567 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30292 | SCR_003010 | SciCrunch Registry | Cancer Genomics Publication | 2026-09-19 12:58:35 | 2 | |||||
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EyeBrowse Resource Report Resource Website 1+ mentions |
EyeBrowse (RRID:SCR_008000) | data or information resource, data set |
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 | SciCrunch Registry | EyeBrowse | 2026-09-19 12:58:39 | 3 | |||||||
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CistromeFinder Resource Report Resource Website 1+ mentions |
CistromeFinder (RRID:SCR_005405) | CistromeFinder | data or information resource, data set | 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 | SciCrunch Registry | 2026-09-19 12:58:37 | 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 or information resource, data set | 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 | SciCrunch Registry | 2026-09-19 12:58:39 | 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) | access service resource, core facility, 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 | SciCrunch Registry | VUB ICMIC | 2026-09-19 12:58:40 | 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 | access service resource, core facility, 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 | SciCrunch Registry | CFG, University at Albany DNA Microarray Core Facility, University at Albany, UAlbany, Functional Genomics, Center for Functional Genomics, DNA Microarray | 2026-09-19 12:59:10 | 0 | |||||||
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Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility Resource Report Resource Website 10+ mentions |
Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility (RRID:SCR_014847) | GT3 | access service resource, core facility, service resource | Core facility that provides consultation on the use of viral vector technologies as well as custom design and production services for multiple vector types. The GT3 facilitates the use of these research tools by Salk researchers and others across diverse fields of study such as systems neuroscience, stem cell biology, metabolism, ageing, cancer biology and gene therapy. The GT3 core is a designated Cancer Center Council (C3) core facility. Cancer Center members from participating C3 institutes have preferential rates. | core facility, gene, vector, viral vector, manipulation, gene therapy, cancer, stem cell |
is listed by: ABRF CoreMarketplace has parent organization: Salk Institute for Biological Studies |
NINDS R24 Core Grant ; NEI ; Salk Institute GT3 Core Facility ; NCI CCSG P30 014195; NINDS R24NS092943 |
Restricted | ABRF_1642 | https://coremarketplace.org/?FacilityID=1642&citation=1 | SCR_014847 | SciCrunch Registry | , Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core (GT3), Salk Institute Gene Transfer Targeting and Therapeutics Core | 2026-09-19 12:59:15 | 10 | |||||
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Salk Institute Functional Genomics Core Facility Resource Report Resource Website |
Salk Institute Functional Genomics Core Facility (RRID:SCR_014841) | FGL | access service resource, core facility, 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 | SciCrunch Registry | 2026-09-19 12:59:15 | 0 | |||||||||
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CellTax vignette Resource Report Resource Website 1+ mentions |
CellTax vignette (RRID:SCR_017000) | data or information resource, data set | Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing. | data, classification, cell, type, mammalian, brain, cellular, taxonomy, mouse, visual, cortex, gene, expression, pattern, cortical, region |
is related to: Allen Brain Atlas API is related to: Allen Mouse Brain Reference Atlas is related to: Allen Cell Types Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science ; NEI R01 EY023173; NIMH U01 MH105982 |
PMID:26727548 | Free, Public | SCR_017000 | SciCrunch Registry | Cellular Taxonomy of the Mouse Visual Cortex, Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science | 2026-09-19 12:59:27 | 3 | |||||||
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Massachusetts University Medical School Transgenic Animal Modeling Core Facility Resource Report Resource Website |
Massachusetts University Medical School Transgenic Animal Modeling Core Facility (RRID:SCR_017729) | TAMC | access service resource, core facility, service resource | Core to produce genetically modified mice, rats, and stem cells for the UMMS Scientific Community.Composed of two facilities: Animal Modeling Facility and Gene Targeting and Stem Cell Facility. | Genetically, modified, mice, rat, stem, cell, gene, targeting, core, facility | University of Massachusetts Medical School | Restricted | ABRF_146 | SCR_017729 | SciCrunch Registry | Transgenic Animal Modeling Core | 2026-09-19 12:59:28 | 0 | |||||||
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Stanford Diabetes Research Center Diabetes Genomics Analysis Core Resource Report Resource Website 1+ mentions |
Stanford Diabetes Research Center Diabetes Genomics Analysis Core (RRID:SCR_016213) | GDAC, SDRC-GDAC, SDRC | access service resource, core facility, service resource | Core facility that offers library preparation and sequencing services on a variety of platforms - Illumina HiSeq 4000, MiSeq, HiSeq 2500 and PacBio Sequel - as well as bioinformatics analysis. It can sequence a variety of commercial sample preparation kits as well as custom workflows. DGAC provides access to high throughput sequencing and analysis to researchers at the Stanford Diabetes Research Center. | library, sequence, workflow, bioinformatic, gene, analysis, sequencing |
is related to: Stanford Diabetes Research Center Diabetes Immune Monitoring Core is related to: Stanford Diabetes Research Center Stanford Islet Research Core is related to: Stanford Diabetes Research Center Diabetes Clinical and Translational Core has parent organization: Stanford University; Stanford; California is organization facet of: Stanford Diabetes Research Center |
NIDDK P30 DK116074 | Available to external user | SCR_016213 | SciCrunch Registry | SDRC, Genomics Analysis Core, Diabetes Genomics Analysis Core | 2026-09-19 12:59:27 | 1 | |||||||
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Nebraska University Medical Center Epigenomics Core Facility Resource Report Resource Website |
Nebraska University Medical Center Epigenomics Core Facility (RRID:SCR_017800) | ECF | access service resource, core facility, service resource | Core assists with epigenetic analysis including DNA Methylation, Chromatin Immunoprecipitation and Real Time Quantitative PCR gene expression analysis. Services include DNA Methylation Analysis, Specific Genomic Location Analysis:Methylation Specific PCR,Bisulfite Sequencing,Bisulfite Pyrosequencing,Qiagen PyroMark Pyrosequencer Instrumentation;Genome Wide Analysis:High Throughput Sequencing Methylation Analysis, Methyl-Sensitive Cut Counting (MSCC),Methyl CpG Binding Domain - Isolated Genome Sequencing (MiGS);Chromatin Immunoprecipitation Analysis (ChIP):Analysis of Histone Modifications,DNA-Protein Interactions,Chromatin Positions analyzed using:Quantitative PCR Analysis (Real-Time QPCR),High Throughput Sequencing Analysis (ChIP-Seq);Gene Expression Analysis (QPCR):Real-Time Quantitative PCR Gene Expression. | Epigenetic, analysis, DNA, methylation, ChIP, RT PCR, gene, expression, service, core | Open | ABRF_458 | SCR_017800 | SciCrunch Registry | Epigenomics Core Facility | 2026-09-19 12:59:30 | 0 | ||||||||
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Garvan Institute of Medical Research Molecular Genetics Core Facility Resource Report Resource Website |
Garvan Institute of Medical Research Molecular Genetics Core Facility (RRID:SCR_017849) | access service resource, core facility, service resource | Core facility for high throughput services covering the areas of Capillary Sequencing, Mouse Genotyping, SNP Genotyping, Clinical Diagnostic Sequencing, Cell Line Identification, Gene Expression Analysis and DNA/RNA extraction. | Molecular, genetics, capillary, sequencing, mouse, genotyping, SNP, clinical, diagnosis, cell, line, identification, gene, expression, analysis, DNA, RNA, extraction, service, core, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: Garvan Institute of Medical Research |
Open | ABRF_656 | SCR_017849 | SciCrunch Registry | Garvan's Genetics Core Facility | 2026-09-19 12:59:32 | 0 |
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