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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | database, catalog, data set, service resource, data or information resource, narrative resource, standard specification | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NHGRI U01 HG004597; NHGRI U41HG007050; NIDA ; OBSSR ; NIMH ; NHLBI ; NIMHD ; TRSP ; NHGRI U24 HG012556; ODP ; NINDS ; NCI |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-02-15 09:19:30 | 61 | ||||
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CHASM/SNV-Box Resource Report Resource Website 1+ mentions |
CHASM/SNV-Box (RRID:SCR_006445) | CHASM/SNV-Box | data or information resource, database, software resource | CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning. | is listed by: OMICtools | Cancer | NCI CA152432; NCI CA135866; NSF DBI0845275 |
Acknowledgement requested, Free, Non-commercial | OMICS_00127 | SCR_006445 | CHASM / SNV-Box, Cancer-specific High-throughput Annotation of Somatic Mutations | 2026-02-15 09:19:15 | 3 | ||||||
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Transdisciplinary Tobacco Use Research Centers Resource Report Resource Website |
Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) | TTURC | disease-related portal, topical portal, data or information resource, portal | A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment. | gene, genetic factor, addiction gene, behavioral treatment, biomarker, molecule, nicotine use disorder, prevention, psychosocial factor, smoking, smoking cessation, tobacco exposure, treatment, nicotine, prevention, tobacco, intervention | has parent organization: National Cancer Institute | Nicotine use disorder, Addiction | NCI ; NIDA ; NIAAA |
nif-0000-24133 | SCR_006858 | 2026-02-15 09:19:23 | 0 | |||||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | web service, web application, data access protocol, software resource | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-02-15 09:19:21 | 2760 | ||||
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Duke Cancer Institute Resource Report Resource Website 1+ mentions |
Duke Cancer Institute (RRID:SCR_004338) | DCI | topical portal, data or information resource, portal | One of 40 centers in the country designated by the National Cancer Institute (NCI) as a comprehensive cancer center, it combines cutting-edge research with compassionate care. Its vision is to accelerate research advances related to cancer and improve Duke''s ability to translate these discoveries into the most advanced cancer care to patients by uniting hundreds of cancer physicians, researchers, educators, and staff across the medical center, medical school, and health system under a shared administrative structure. | cancer, patient, research, clinical trial |
is related to: Biospecimen Repository and Processing Core has parent organization: Duke University School of Medicine; North Carolina; USA is parent organization of: DCI Tissue and Blood Procurement Shared Resource |
Cancer | NCI | nlx_143695 | http://www.cancer.duke.edu/ | SCR_004338 | Duke Cancer Institute: A National Cancer Institute-designated Comprehensive Cancer Center | 2026-02-15 09:18:41 | 1 | |||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | source code, database, software resource, service resource, storage service resource, data repository, production service resource, data or information resource, analysis service resource | An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket. | stem cell, analysis, cancer stem cell, galaxy, gene, pathway, molecular signature, tissue, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard T.H. Chan School of Public Health |
Cancer | NCI 1RC2CA148222-01 | PMID:22121217 | Free, The community can contribute to this resource | biotools:scde_discovery, nlx_44656 | https://bio.tools/scde_discovery | SCR_004453 | Harvard Stem Cell Discovery Engine, SCDE - Stem Cell Discovery Engine | 2026-02-15 09:18:43 | 57 | |||
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Case Western Reserve University Case Comprehensive Cancer Center Resource Report Resource Website |
Case Western Reserve University Case Comprehensive Cancer Center (RRID:SCR_004387) | Case CCC, CWRU Case CCC | portal, service resource, core facility, data or information resource, access service resource, topical portal | Core is a partnership organization supporting all cancer-related research efforts at CWRU, University Hospitals Case Medical Center, and the Cleveland Clinic. The Case CCC is organized into 9 interdisciplinary scientific programs plus one program initiative. Research programs of the Case CCC are extending into CWRU affiliated hospitals including MetroHealth Medical Center (the region's county hospital), Louis Stokes Veterans Affairs Hospital, and 13 community medical centers operated by University Hospitals and Cleveland Clinic. The Center operates an NCI-supported Cancer Information Service (CIS) serving the northern half of Ohio as part of the Midwest consortium and has an active outreach program for clinical practice-based prevention and screening initiatives, educational programs, minority recruitment, and facilitation of patient referrals. Case CCC is a member of NCI's CaBIG initiative and is actively pursuing electronic databases for clinical trials, tissue repositories, and related bioinformatics. |
has parent organization: Case Western Reserve University; Ohio; USA is parent organization of: Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility |
NCI | Available to external user | nlx_40003 | SCR_004387 | 2026-02-15 09:18:46 | 0 | ||||||||
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Repository of molecular brain neoplasia data Resource Report Resource Website 1+ mentions |
Repository of molecular brain neoplasia data (RRID:SCR_004704) | REMBRANDT | portal, data analysis service, database, service resource, production service resource, data or information resource, topical portal, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotype |
is related to: Gene Ontology is related to: Glioma Molecular Dignostic Initiatives has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI ; NINDS |
PMID:19208739 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00230 | SCR_004704 | REMBRANDT (Repository of Molecular Brain Neoplasia Data), REMBRANDT - Repository of Molecular Brain Neoplasia Data, REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) | 2026-02-15 09:18:47 | 2 | ||||
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SEAHORSE Resource Report Resource Website |
SEAHORSE (RRID:SCR_027399) | data or information resource, database | Web-based database and search tool for exploratory data analysis in which we have pre-computed statistical associations between available data elements. Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive clinical and phenotypic information. Allows users to explore significant associations using tabulated summary statistics, data visualizations, and functional enrichment analyses (using RNA-seq data) for identified sets of genes. | Unexpected Correlations, Large Cohort Studies, Gene Expression, Gene Regulatory Networks, Correlations | NCI R35 CA220523; NHGRI R01 HG011393; NCI U24 CA231846 |
DOI:10.1101/2025.08.15.670514v1 | Free, Freely available, | SCR_027399 | Serendipity Engine Assaying Heterogeneous Omics Related Sampling Experiments | 2026-02-14 02:09:30 | 0 | ||||||||
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SMD Resource Report Resource Website 10+ mentions |
SMD (RRID:SCR_004987) | SMD | data analysis service, database, service resource, storage service resource, data repository, production service resource, data or information resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser. | data set, microarray, gene, image, gene expression, adenovirus disease, apoptosis, leukemia, source code, web service |
is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: Longhorn Array Database is related to: Tuberculosis Database has parent organization: Princeton University; New Jersey; USA is parent organization of: SOURCE |
NCI ; Howard Hughes Medical Institute ; Stanford University School of Medicine; California; USA ; NHGRI R01 HG003469 |
PMID:18953035 PMID:17182626 PMID:15608265 PMID:12519956 PMID:11125075 |
Public, Open-source license, The community can contribute to this resource, Acknowledgement requested, THIS RESOURCE IS NO LONGER IN SERVICE | nlx_94141, OMICS_00870, r3d100010555 | https://doi.org/10.17616/R3DW40 | http://genome-www.stanford.edu/microarray/, http://smd.stanford.edu/ | SCR_004987 | Stanford Microarray Database | 2026-02-15 09:18:52 | 12 | |||
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WebArrayDB Resource Report Resource Website 1+ mentions |
WebArrayDB (RRID:SCR_005577) | WebArrayDB | data analysis service, database, software resource, service resource, storage service resource, production service resource, data repository, data or information resource, analysis service resource | An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters. | is listed by: OMICtools | Prostate Cancer Foundation ; Mary Kay Ash Foundation ; NIH ; NIAI R01AI034829; NIAI R01AI052237; NCI R01CA68822; NCI U01CA114810 |
PMID:19602526 | Open source, Account required, The software package is available for the use on a public web server or can be downloaded | OMICS_00782 | SCR_005577 | 2026-02-15 09:19:07 | 8 | |||||||
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PeptideMapper Resource Report Resource Website 1+ mentions |
PeptideMapper (RRID:SCR_005763) | PeptideMapper | web service, data access protocol, software resource | The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter. | peptide, sequence, protein, alignment, expressed sequence tag, mrna, est, htc, genbank, refseq, uniprot, ipi, vega, embl, hinvdb | has parent organization: Edwards Lab | NCI CA126189 | PMID:17437027 | nlx_149229 | SCR_005763 | PeptideMapper Web-Service, Peptide Mapper | 2026-02-15 09:19:02 | 4 | ||||||
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SCSORS - Semi-Custom Synthesis On-line Request System Resource Report Resource Website 1+ mentions |
SCSORS - Semi-Custom Synthesis On-line Request System (RRID:SCR_005636) | SCSORS | service resource, reagent manufacture, material service resource, production service resource | ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years. | compound, pharmaceutical, chemistry, drug discovery, research | NCI | nlx_146249 | SCR_005636 | SCSORS Project, Semi-Custom Synthesis On-line Request System | 2026-02-15 09:19:01 | 1 | ||||||||
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CGAP GO Browser Resource Report Resource Website 1+ mentions |
CGAP GO Browser (RRID:SCR_005676) | CGAP GO Browser | data or information resource, data set, service resource | With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool | gene, biological process, cellular component, molecular function, browser, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Cancer Genome Anatomy Project |
NCI | Free for academic use | nlx_149116 | SCR_005676 | Cancer Genome Anatomy Project GO Browser | 2026-02-15 09:19:01 | 4 | ||||||
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Gene Set Enrichment Analysis Resource Report Resource Website 10000+ mentions |
Gene Set Enrichment Analysis (RRID:SCR_003199) | GSEA | software application, data processing software, software resource, software toolkit, data analysis software | Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes. | gene, expression, profile, pathway, data, set, phenotype, genome, enrichment, RNA, analysis, bio.tools, bio.tools |
is used by: Molecular Signatures Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GoMapMan has parent organization: Broad Institute |
NCI ; NIH ; NIGMS |
PMID:16199517 | Free, Freely available | nif-0000-30629, SCR_016882, biotools:gsea, OMICS_02279 | http://www.broad.mit.edu/gsea https://bio.tools/gsea |
SCR_003199 | GSEA, Gene Set Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-02-15 09:18:30 | 18865 | ||||
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Weighted Gene Co-expression Network Analysis Resource Report Resource Website 1000+ mentions |
Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) | WGCNA | software application, data processing software, data analysis software, software resource | Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, co-expression, analysis, network, bio.tools, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
NCI P50CA092131; NIDA 1R01DA030913-01; NIDCR R01DE019255; NIAID U19 AI063603-01 |
PMID:19114008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31889, biotools:crosslinkwgcna | http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation https://bio.tools/crosslinkwgcna |
SCR_003302 | WGCNA: an R package for weighted correlation network analysis | 2026-02-15 09:18:32 | 1860 | ||||
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Glioma Molecular Dignostic Initiatives Resource Report Resource Website 10+ mentions |
Glioma Molecular Dignostic Initiatives (RRID:SCR_003329) | GMDI | service resource, storage service resource, data repository, data or information resource, narrative resource, standard specification, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. An initiative to develop a molecular classification schema that is both clinically and biologically meaningful, based on gene expression and genomic data from tumors (Gliomas) of patients who will be prospectively followed through natural history and treatment phase of their illness. The study will also explore gene expression profiles to determine the responsiveness of the patients and correlate with discrete chromosomal abnormalities. The initiative was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. The sample collection is accompanied by careful and prospective clinical data acquisition, allowing a variety of matched molecular and clinical data permitting a wide variety of analyses. GMDI has accrued fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and fresh frozen tumors in the prospective phase (from a variety of institutions). In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory. | molecular neuroanatomy resource, molecular data, clinical data, genomic analyses, genomics, gene, expression array, snp array, gene expression, microarray, glioma initiating cell, glioma stem cell, protein, glioma, molecular, diagnostic, dna, rna, tumor, tissue, blood, plasma, data repository |
is listed by: One Mind Biospecimen Bank Listing is related to: Repository of molecular brain neoplasia data has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31950 | http://search.engrant.com/project/NxvG9G/the_glioma_molecular_diagnostic_initiative_characterizing_brain_tumor_data | SCR_003329 | Glioma Molecular Diagnostic Initiative: Characterizing Brain Tumor Data | 2026-02-15 09:18:29 | 17 | ||||
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CHISEL Resource Report Resource Website 1+ mentions |
CHISEL (RRID:SCR_023220) | CHISEL | software application, software resource | Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers. | infer allele and haplotype specific copy numbers, individual cells, low coverage single cell DNA sequencing data, weak allelic signals, weak signals integration, | NHGRI R01HG007069; NCI U24CA211000; NSF CCF 1053753; Chan Zuckerberg Initiative DAF grants ; NCI P30CA072720; O’Brien Family Fund for Health Research ; Wilke Family Fund for Innovation |
DOI:10.1038/s41587-020-0661-6 | Free, Available for download, Freely available | SCR_023220 | Copy-number Haplotype Inference in Single-cell by Evolutionary Links | 2026-02-15 09:23:01 | 2 | |||||||
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TEtranscripts Resource Report Resource Website 10+ mentions |
TEtranscripts (RRID:SCR_023208) | software toolkit, software resource | Software package for including transposable elements in differential enrichment analysis of sequencing datasets. Used for including transposable elements in differential expression analysis of RNA-seq datasets. RNAseq TE quantification tool. | Transposable Elements, transposable elements, RNAseq TE, sequencing datasets, RNAseq TE quantification | uses: DESeq2 | Rita Allen Foundation ; NSF MCB 1159098; NCI CA 045508 |
PMID:26206304 | Free, Available for download, Freely available | SCR_023208 | 2026-02-15 09:23:01 | 15 | ||||||||
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RPCI Gene Targeting and Transgenic Shared Resource Resource Report Resource Website |
RPCI Gene Targeting and Transgenic Shared Resource (RRID:SCR_001020) | access service resource, core facility, service resource | Facility which provides researchers with transgenic mouse technologies, methods, and animal models. Knockout mice, transgenic mice, and mice on multiple strain backgrounds are provided. | core facility, mouse, animal model, transgenic, knockout, cancer, shared resource |
is listed by: ScienceExchange has parent organization: Roswell Park Cancer Institute |
NCI P30CA16056 | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_10094 | http://www.scienceexchange.com/facilities/gene-targeting-and-transgenic-facility | SCR_001020 | RPCI Gene Targeting and Transgenic Facility, Roswell Park Cancer Institute Gene Targeting and Transgenic Facility, Roswell Park Cancer Institute Gene Targeting and Transgenic Shared Resource | 2026-02-15 09:18:01 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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