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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UC Davis Genome Center Labs and Facilities Resource Report Resource Website 1+ mentions |
UC Davis Genome Center Labs and Facilities (RRID:SCR_012480) | UCD Genome Center Labs & Facilities, UCD Genome Center Labs and Facilities | training service resource, core facility, portal, data or information resource, organization portal, service resource, access service resource | Genome Center uses technologies to understand how heritable genetic information of diverse organisms functions in health and disease. Provides research facilities, service cores, and staff for genomics research and training. Core facilities for Bioinformatics,DNA Technologies and Expression Analysis, Metabolomics, Proteomics,TILLING Core,Yeast One Hybrid Services Core. | Heritable, genetic, information, diverse, organism, function, health, disease, core, facility, service, genomic, training, |
is listed by: ScienceExchange is related to: University of California at Davis Genome Center Proteomics Core Facility has parent organization: University of California at Davis; California; USA |
SciEx_227, SciEx_756, SCR_012659 | https://genomecenter.ucdavis.edu/ | http://www.scienceexchange.com/facilities/uc-davis-genome-center-uc-davis | SCR_012480 | University of California Davis Genome Center Labs and Facilities, UC Davis Genome Center Labs & Facilities, University of California Davis Genome Center Labs & Facilities | 2026-02-14 02:04:49 | 1 | ||||||
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software resource, software library, software toolkit, software application | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | 2026-02-14 02:04:35 | 77 | ||||||||
|
SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/ https://bio.tools/SnpHub |
SCR_018177 | 2026-02-14 02:03:34 | 1 | |||||||
|
genomics resource for animal lectins Resource Report Resource Website 1+ mentions |
genomics resource for animal lectins (RRID:SCR_018122) | data or information resource, portal, topical portal | Resource presents information about animal lectins involved in various sugar recognition processes. | Genomic, animal lectin, sugar recognition process | has parent organization: Imperial College London; London; United Kingdom | BBSRC ; Wellcome Trust ; Consortium for Functional Glycomics |
Free, Freely available | SCR_018122 | 2026-02-14 02:03:31 | 3 | |||||||||
|
MITE-Tracker Resource Report Resource Website 1+ mentions |
MITE-Tracker (RRID:SCR_017030) | MITE Tracker | sequence analysis software, data processing software, data analysis software, software application, software resource | Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences. | genomic, sequence, discover, miniature, inverted, repeat, transposable, element, clustering, cdhit |
uses: NCBI BLAST is listed by: OMICtools is related to: Python Programming Language |
National Institute of Agricultural Technology ; National Council for Science and Technology ; Argentina |
DOI:10.1186/s12859-018-2376-y | Free, Available for download, Freely available | OMICS_32242 | SCR_017030 | MITE Tracker, Miniature Inverted repeats Transposable Elements Tracker | 2026-02-14 02:03:22 | 3 | |||||
|
University of North Carolina Charlotte Bioinformatics Services Division Resource Report Resource Website |
University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) | BiSD, UNC Charlotte BiSD | data analysis service, core facility, analysis service resource, data or information resource, production service resource, service resource, access service resource | Core to assist with analyzing and interpreting data produced by genomic technologies. | bioinformatics, analysis, data, genomic | Open | SCR_017182 | , Charlotte, University of North Carolina, BiSD, Bioinformatics Services Division, UNC | 2026-02-14 02:03:24 | 0 | |||||||||
|
City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) | IGBC | data analysis service, core facility, analysis service resource, data or information resource, production service resource, service resource, access service resource | Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators. | bioinformatics, genomic, data, analysis, service, next, sequencing | Restricted | SCR_017188 | , City of Hope, Integrative Genomics and Bioinformatics Core, Bioinformatics Core Facility, National Medical Center, IGBC | 2026-02-14 02:03:21 | 1 | |||||||||
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SeQuiLa Resource Report Resource Website 1+ mentions |
SeQuiLa (RRID:SCR_017220) | data analysis software, software resource, data processing software, software application | Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals. | genomic, intervals, querying, processing, Apache, Spark, SQL, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Warsaw University of Technology; Warsaw; Poland |
National Science Center ; Polish budget funds for science |
PMID:30428005 | Free, Available for download, Freely available | biotools:SeQuiLa-cov | http://biodatageeks.org/sequila/ https://bio.tools/SeQuiLa-cov |
SCR_017220 | 2026-02-14 02:03:25 | 1 | ||||||
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University of Manchester Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) | Manchester Bioinformatics Facility | data analysis service, core facility, analysis service resource, production service resource, service resource, software resource, access service resource | Core provides assistance in integrative analysis of genomic datasets to support faculty. | bioinformatics, analysis, genomic, data, dataset | has parent organization: University of Manchester; Manchester; United Kingdom | Restricted | SCR_017171 | , Bioinformatics Facility, University of Manchester, Bioinformatics Core Facility | 2026-02-14 02:03:15 | 2 | ||||||||
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Glomerular Disease Study & Trial Consortium Resource Report Resource Website 1+ mentions |
Glomerular Disease Study & Trial Consortium (RRID:SCR_017264) | GlomCon | portal, consortium, data or information resource, organization portal, disease-related portal, topical portal | Consortium to bring together clinicians, pathologists, researchers, and biotech innovators to create scalable network of stakeholders interested in helping patients with glomerular kidney disease. Makes collective expertise of its members available for discussion of individual cases, provides infrastructure for biomarker studies, enables genomic research, and facilitates clinical trials. | glomerular, kidney, disease, biomarker, genomic, clinical, trial | glomerular kidney disease | Restricted | SCR_017264 | 2026-02-14 02:03:23 | 4 | |||||||||
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Analysis, Visualization, and Informatics Lab-space (AnVIL) Resource Report Resource Website 10+ mentions |
Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) | AnVIL | data repository, storage service resource, portal, data or information resource, service resource, project portal | Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces. | Dataset, NHGRI, program, NIH, initiative, funded, human, genomic, data, access, sharing, FAIR, analysis, workflow |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIH | Restricted | https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL | SCR_017469 | Visualization, and Informatics Lab-space, AnVIL, Analysis Visualization and Informatics Lab-space, Analysis | 2026-02-14 02:03:12 | 24 | ||||||
|
TCGAbiolinks Resource Report Resource Website 50+ mentions |
TCGAbiolinks (RRID:SCR_017683) | data analysis software, software resource, data processing software, software application | Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R. | Integrative, analysis, TCGA data, cancer, genome, atlas, genomic, analysis, expression, methylated, region, survival plot, phenotype, tumor, epigenomic, alteration, clinical, molecular, retrival | BridgeIRIS ; INNOVIRIS ; Region de Bruxelles Capitale ; Brussels ; Belgium ; GENGISCAN ; São Paulo Research Foundation |
PMID:26704973 DOI:10.12688/f1000research.8923.2 |
Free, Available for download, Freely available | https://github.com/BioinformaticsFMRP/TCGAbiolinks | SCR_017683 | Cancer Genome Atlas (TCGA) biolinks | 2026-02-14 02:03:28 | 93 | |||||||
|
tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | data analysis service, analysis service resource, production service resource, service resource, software toolkit, software resource | Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis. | analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation | Free, Available for download, Freely available | SCR_016957 | 2026-02-14 02:04:38 | 11 | |||||||||||
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Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | data repository, storage service resource, portal, data or information resource, organization portal, service resource, disease-related portal, topical portal, database | Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ; NIH |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1 https://commonfund.nih.gov/kidsfirst |
SCR_016493 | Data Resource Portal | 2026-02-14 02:04:57 | 3 | ||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, software resource, data processing software, software application | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder https://bio.tools/OrthoFinder https://bio.tools/OrthoFinder |
SCR_017118 | OrthoFinder2, OrthoFinder | 2026-02-14 02:04:35 | 2899 | |||||
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ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data visualization software, data processing software, data analysis software, software application, software resource | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Cancer Research Center-Heidelberg Center for Personalized Oncology ; BMBF |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap https://bio.tools/complexheatmap |
SCR_017270 | 2026-02-14 02:04:35 | 3266 | ||||||
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Seurat Resource Report Resource Website 5000+ mentions |
Seurat (RRID:SCR_016341) | data processing software, data analysis software, software toolkit, software application, software resource | Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers |
PMID:29608179 | Free, Available for download, Freely available | https://github.com/satijalab/seurat | SCR_016341 | 2026-02-14 02:04:51 | 9395 | ||||||||
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Ximmer Resource Report Resource Website 1+ mentions |
Ximmer (RRID:SCR_016427) | data visualization software, data processing software, data analysis software, software application, software resource, simulation software | Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data. | cnv, copy, number, variant, exome, targeted, sequencing, data, next, generation, genomic | is listed by: OMICtools | National Human Genome Research Institute ; National Eye Institute ; National Heart Lung and Blood Institute ; Australian National Health and Medical Research Council ; Victorian State Government |
DOI:10.1101/260927 | Open source, Free, Available for download, Freely available | https://omictools.com/ximmer-tool http://ximmer.org |
SCR_016427 | 2026-02-14 02:03:15 | 4 | |||||||
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CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | data or information resource, software resource, database, web application | Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network. | marmoset, data, genomic, expression, alternative, splicing, animal, model, neuropsychiatry, social, behavior, ontology, protein, network | Amazonas State Research Support Foundation ; Federal University of Rio Grande do Norte ; Brain Institute ; Multidisciplinary Environment ; NPAD/UFRN ; Brazilian Council for Research and Technological Development |
Free, Freely available | SCR_016506 | 2026-02-14 02:03:16 | 1 | ||||||||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | web service, organism-related portal, portal, data or information resource, data access protocol, software resource, topical portal, database, project portal | Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. | project, genomic, information, fungi, data, sequence, energy, environment |
is related to: MycoCosm is related to: Lawrence Berkeley National Laboratory has parent organization: DOE Joint Genome Institute |
the DOE Office of Biological and Environmental Research (BER) | Free, Register for an account | SCR_016463 | 2026-02-14 02:03:16 | 2 |
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