What do I do with my genotype / phenotype data?
- Diversity Outbred Database (DODB), citation: https://dodb.jax.org - DODB provides a location for investigators to submit their DO experiments including associated genotype array data (MUGA platforms), clinical phenotype data, associated publication(s) and other types of supporting data such as: RNA expression, eQTL, proteomics, metabolomics, etc... The download interface acts as the primary entry point for researchers who want to interrogate existing DO studies that have been submitted. There is also an application programming interface (API) to allow data analysts to pull study information from languages like R or Python. DODB allows searching genotype and phenotype data for DO experiments by Publication, Investigator, Project, associated data types submitted with projects, and provides the ability to download full studies or subsets of studies in zipped CSV or R/QTL2 formats. While a user can download subsets of a study's samples, genotypes or phenotypes; other supporting data such as expression, proteomic and metabalomic data are provided as whole project file downloads. As the DODB query interface evolves to be the Diversity platform's entry point for interrogating data, we will begin to allow a user to launch some analysis pipelines, and have visualization endpoints allowing a user to explore the analyzed results (QTLViewer being an example endpoint).
- Mouse Phenome Database, https://phenome.jax.org/ - A highly curated phenotype data repository and analysis platform for experimental mouse data. This will be the primary repository for data from BXD, CC and DO phenotyping experiments. Part of our current initiative is to fully integrate MPD and DODB, so that data submissions for the two web applications are collected through one intake and curation platform, ensuring that data is stored once, is consistent and well curated between the two specialized applications. We are also planning integration between the two interfaces so that a user is taken to the tool that best meets their investigative needs. The data intake and curation platform that is currently under development will allow an investigator to submit their data online, and do some initial self curation before submitting the data to our team of professional curators.
- QTL Viewer, source code: https://github.com/churchill-lab/qtlweb, example instance for DO Islet: https://churchilllab.jax.org/qtlviewer/attie/islets (associated with paper: Keller, et al. Genetic Drivers of Pancreatic Islet Function, PMID 29567659) - QTL Viewer is an interactive web-based analysis tool that will allow users to replicate the analyses reported for a study (in the example link, the afore mentioned paper). It includes the ability to search various subsets of data from a study such as phenotypes or expression data and then visualize data with profile, correlation, LOD, effect, mediation and SNP association plots.
- HaploQA - https://haploqa.jax.org/ - A web application for performing haplotype analysis of genotype calls from the “MUGA” platform genotyping arrays. The application was developed at the Jackson Laboratory to facilitate genetic quality assurance of mice using genotype data derived from these platforms. The tool allows the community to examine data sets which have been publicly released by viewing Karoytype plots generated by haplotype reconstructions. An individual can also contact the team to register and receive an account, which will allow them to upload their own data (MegaMUGA or GigaMUGA genotypes), have haplotype reconstructions run, and examine their data using a private account, and if they choose, share that data publicly. An individual can also set up their own private instance, with source code available here: https://github.com/TheJacksonLaboratory/haploqa
- GeneNetwork, http://www.genenetwork.org/ - GeneNetwork is a web based genetics platform, formally known as WebQTL. This is considered to be the primary web platform for searching and interrogating data from BXD lines.
R/qtl2, https://kbroman.org/qtl2/ - An R package for QTL analysis for high-dimensional data and complex crosses. This is a reimplementation of the QTL analysis software R/qtl, to better handle these types of data. We consider this to be the de facto package for command-line analysis of DO data.
For questions associated with these tools, send email to firstname.lastname@example.org.