GAC

UW Genetic Analysis Center

Seattle, WA

Pinned Repositories

analysis_pipeline
TOPMed analysis pipeline
Language:R52 12 1931
analysis_pipeline_cwl
CWL for running analysis pipeline scripts as workflows
Language:Common Workflow Language3 4 111
aws_s3
scripts to copy data to s3 and utilize sqs
Language:Python4 7 03
GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Language:R35 8 5814
gregor_data_models
A repository for version control of consortium data model(s)
Language:R9 7 183
simulate_phenotypes
Code for simulating phenotypes
Language:R3 6 06
topmed-dcc-harmonized-phenotypes
Documentation for the TOPMed DCC's harmonized phenotypes
Language:R7 6 04
topmed_workshop_2017
Course materials for the TOPMed Analysis Workshop, August 7-9, 2017
Language:R4 10 76
topmed_workshop_2018
Course materials for SISG Module 12: Computational Pipeline for WGS Data, July 18-20, 2018
Language:R5 9 137
wgsaparsr
Code for parsing TOPMED variant annotation files produced by the WGSA annotation tool.
Language:R5 5 1213

GAC's Repositories

UW-GAC/GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Language:R35 8 5814
UW-GAC/gregor_data_models
A repository for version control of consortium data model(s)
Language:R9 7 183
UW-GAC/simulate_phenotypes
Code for simulating phenotypes
Language:R3 6 06
UW-GAC/primed_data_models
A repository for version control of consortium data model(s)
Language:R2 4 122
UW-GAC/AnvilDataModels
R package to work with AnVIL data models
Language:R1 4 200
UW-GAC/django-anvil-consortium-manager
Django app to manage AnVIL workspace permissions
Language:Python1 4 1550
UW-GAC/gregor-data-tracking
Code to support data tracking and reporting for GREGoR
Language:Jupyter Notebook1 5 2
UW-GAC/pip-tools-actions
Github actions for pip-tools
1 1 0
UW-GAC/primed-file-conversion
PRIMED file conversion workflows
Language:WDL1 3 0
UW-GAC/primed_example_notebooks
Example notebooks for working with PRIMED data in AnVIL workspaces
Language:HTML1 4 1
UW-GAC/anvil-util-workflows
Utilities for checking files in AnVIL
Language:WDL0 3 52
UW-GAC/gregor-django
GREGoR Consortium Django application website
Language:Python0 5 540
UW-GAC/primed-django
PRIMED Consortium Django application website
Language:Python0 5 860
UW-GAC/SISG_2024
Language:HTML02
UW-GAC/dbgap_xml_parser
Language:R2 3
UW-GAC/fetch-dbgap-files
Code to fetch dbGaP files using sra-toolkit
Language:Python2 01
UW-GAC/genesis_wdl
WDL workflow for analysis based on the R GENESIS package
Language:R1 0
UW-GAC/gregor-file-checks
GREGoR file checking workflows
Language:WDL6 4
UW-GAC/gregor_example_notebooks
Example notebooks and code for working with GREGoR data in AnVIL workspaces.
Language:R3 2
UW-GAC/gregor_wgs_processing
wgs reprocessing scripts
Language:WDL1 0
UW-GAC/parse-dbgap-application
Python code to parse DARs out of a dbGaP application PDF
Language:Python2 1
UW-GAC/pgsc_calc_wdl
WDL wrapper for the pgsc_calc workflow
Language:WDL
UW-GAC/primed-bcftools
Language:WDL3 0
UW-GAC/primed-file-checks
PRIMED file checking workflows
Language:WDL4 5
UW-GAC/primed-genesis-gwas
Workflow for running GENESIS on PRIMED data
Language:WDL3 0
UW-GAC/primed-imputation
PRIMED imputation workflow
Language:WDL3 0
UW-GAC/primed-inventory-workflows
Workflows for generating the PRIMED inventory workspace
Language:R3 0
UW-GAC/primed-pgs-queries
Code to query the PGS catalog for PRIMED PMIDs
Language:Python2 3
UW-GAC/wdl_test
Language:WDL4 0
UW-GAC/womtool-action
Run womtool as a github action
1 0