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http://cre.jax.org/index.html

Repository of Cre Driver lines and related information resources. Their services include analysis of Cre line excision function in both target and non-target tissues using Cre reporter lines and presenting the annotated data in the expression data portion of this website, http://cre.jax.org/data.html.

Proper citation: JAX Cre Repository (RRID:SCR_005566) Copy   

•   Source: SciCrunch Registry

http://www.primate.wisc.edu/

Research center aimed towards increasing understanding of basic primate biology and improving human health and quality of life. Its goals include helping discover treatments, preventative measures and cures for human disease; gathering knowledge of primate biology and ecosystems; providing resources to scientists world wide; and collecting and disseminating research to the larger scientific community and public.

Proper citation: Wisconsin National Primate Research Center (RRID:SCR_012987) Copy   

•   Source: SciCrunch Registry

http://neurodata.io/

Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.

Proper citation: neurodata (RRID:SCR_014264) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

http://www.wanprc.org/

Center that aims to provide an environment to support biomedical research directed towards human health issues and nonhuman primate health and biology. To meet this mission, the WaNPRC supports biomedical research activities, professional research staff, specifically bred and maintained nonhuman primate colonies, and dedicated facilities and equipment required for nonhuman primate research protocols.

Proper citation: Washington National Primate Research Center (RRID:SCR_002761) Copy   

•   Source: SciCrunch Registry

http://www.nsrrc.missouri.edu/

Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research.

Proper citation: National Swine Resource and Research Center (RRID:SCR_006855) Copy   

•   Source: SciCrunch Registry

http://fit.genomics.lbl.gov/cgi-bin/myFrontPage.cgi

Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function.

Proper citation: Fitness Browser (RRID:SCR_018981) Copy   

•   Source: SciCrunch Registry

https://dgrc.bio.indiana.edu/Home

Serves Drosophila research community by collecting and distributing DNA clones and vectors; collecting and distributing Drosophila cell lines; developing and testing genomics technologies for use in Drosophila and assisting members of the research community in their use.

Proper citation: Drosophila Genomics Resource Center (RRID:SCR_002845) Copy   

•   Source: SciCrunch Registry

https://fgr.hms.harvard.edu/

Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays.

Proper citation: Drosophila RNAi Screening Center (RRID:SCR_000733) Copy   

•   Source: SciCrunch Registry

https://sparc.science

SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short.

Proper citation: SPARC Portal (RRID:SCR_017041) Copy   

•   Source: SciCrunch Registry

https://github.com/aidenlab/juicer.git

Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.

Proper citation: Juicer (RRID:SCR_017226) Copy   

•   Source: SciCrunch Registry

https://amp.pharm.mssm.edu/geneshot/

Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.

Proper citation: Geneshot (RRID:SCR_017582) Copy   

•   Source: SciCrunch Registry

https://github.com/Cai-Lab-at-University-of-Michigan/nTracer

Software tool as plug-in for ImageJ software. Used for tracing microscopic images.

Proper citation: nTracer (RRID:SCR_023032) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/chea3/

Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries.

Proper citation: ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/kea3

Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations.

Proper citation: Kinase Enrichment Analysis 3 (RRID:SCR_023623) Copy   

•   Source: SciCrunch Registry

https://generanger.maayanlab.cloud/gene/A2M?database=ARCHS4

Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types.

Proper citation: GeneRanger (RRID:SCR_023622) Copy   

•   Source: SciCrunch Registry

https://targetranger.maayanlab.cloud/

Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines.

Proper citation: TargetRanger (RRID:SCR_023621) Copy   

•   Source: SciCrunch Registry

https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000674.v1.p1

Human genetics data from an immense (78,000) and ethnically diverse population available for secondary analysis to qualified researchers through the database of Genotypes and Phenotypes (dbGaP). It offers the opportunity to identify potential genetic risks and influences on a broad range of health conditions, particularly those related to aging. The GERA cohort is part of the Research Program on Genes, Environment, and Health (RPGEH), which includes more than 430,000 adult members of the Kaiser Permanente Northern California system. Data from this larger cohort include electronic medical records, behavioral and demographic information from surveys, and saliva samples from 200,000 participants obtained with informed consent for genomic and other analyses. The RPGEH database was made possible largely through early support from the Robert Wood Johnson Foundation to accelerate such health research. The genetic information in the GERA cohort translates into more than 55 billion bits of genetic data. Using newly developed techniques, the researchers conducted genome-wide scans to rapidly identify single nucleotide polymorphisms (SNPs) in the genomes of the people in the GERA cohort. These data will form the basis of genome-wide association studies (GWAS) that can look at hundreds of thousands to millions of SNPs at the same time. The RPGEH then combined the genetic data with information derived from Kaiser Permanente''s comprehensive longitudinal electronic medical records, as well as extensive survey data on participants'' health habits and backgrounds, providing researchers with an unparalleled research resource. As information is added to the Kaiser-UCSF database, the dbGaP database will also be updated.

Proper citation: Resource for Genetic Epidemiology Research on Adult Health and Aging (RRID:SCR_010472) Copy   

•   Source: SciCrunch Registry

http://upr.eagle-i.net/i/0000012c-9dd1-fddf-95a5-371e80000000

Core facility that provides the following services: Necropsy. The Sabana Seca Field Station (SSFS) is the administrative headquarters for the Caribbean Primate Research Center, or CPRC. This area contains offices, a clinic, and laboratories for reproductive biology and bone densitometry, necropsy and maintenance buildings. It houses rhesus monkeys from the CS colony or from the CS genetic line.

Proper citation: UPR Sabana Seca Field Station Caribbean Primate Research Center (RRID:SCR_010134) Copy   

•   Source: SciCrunch Registry