uw-gac Goto Github PK
Name: GAC
Type: Organization
Bio: UW Genetic Analysis Center
Location: Seattle, WA
Blog: https://www.biostat.washington.edu/research/centers/gac
Name: GAC
Type: Organization
Bio: UW Genetic Analysis Center
Location: Seattle, WA
Blog: https://www.biostat.washington.edu/research/centers/gac
TOPMed analysis pipeline
CWL for running analysis pipeline scripts as workflows
Scripts used for working with TOPMed annotation data
Utilities for checking files in AnVIL
WDL to backup data tables on AnVIL
R package to work with AnVIL data models
Creating NFS on AWS
scripts to copy data to s3 and utilize sqs
json files and python scripts for managing AWS batch services
An R package to parse and reformat the TOPMed website contacts table
CWL app to extract genotypes from a GDS file into a text file
internal code used for organizing files downloaded from dbGaP
A utility class to retrieve information and download files from the dbGaP ftp server.
R package to create and check standard files for dbGaP submission
Helper functions for interacting with the TOPmed phenotype database
Django app to manage AnVIL workspace permissions
Scripts for building docker images
python help functions to help run analysis pipeline, r and r studio in our topmed docker images
Code to fetch dbGaP files using sra-toolkit
Notes and presentations on porting pipeline to GCP/Slurm
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Workflows for GWAS with the GENESIS R package
refactor of GENESIS
null model and association testing code
WDL workflow for analysis based on the R GENESIS package
A shiny app to visualize the output of GENESIS null models.
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