UW-GAC/primed_example_notebooks

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UW-GAC/primed_example_notebooks

UW-GAC

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Example notebooks for working with PRIMED data in AnVIL workspaces

analysis_pipeline

TOPMed analysis pipeline

GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

gregor_data_models

A repository for version control of consortium data model(s)

topmed-dcc-harmonized-phenotypes

Documentation for the TOPMed DCC's harmonized phenotypes

wgsaparsr

Code for parsing TOPMED variant annotation files produced by the WGSA annotation tool.

topmed_workshop_2018

Course materials for SISG Module 12: Computational Pipeline for WGS Data, July 18-20, 2018

aws_s3

scripts to copy data to s3 and utilize sqs

topmed_workshop_2017

Course materials for the TOPMed Analysis Workshop, August 7-9, 2017

docker

simulate_phenotypes

Code for simulating phenotypes

analysis_pipeline_cwl

CWL for running analysis pipeline scripts as workflows

Common Workflow Language

primed_data_models

A repository for version control of consortium data model(s)

QCpipeline

Pipeline for quality control of genotype array data

genesis-workflow

Workflows for GWAS with the GENESIS R package

SeqQCpipeline

Pipeline for quality control of sequencing data

Common Workflow Language

SISG_2023

SISG 2023 Module 18: Computational Pipeline for WGS Data

pie

TOPMed phenotype inventory explorer (PIE)

topmed-gsr-reporting

Code to generate a report about TOPMed GSR processing and upload

aws_ami

dbgaptools

R package to create and check standard files for dbGaP submission

AnvilDataModels

R package to work with AnVIL data models

primed-file-conversion

PRIMED file conversion workflows

SISG_2021

SISG_2019

Course materials for SISG Module 17: Computational Pipeline for WGS Data, July 24-26, 2019

gregor-data-tracking

Code to support data tracking and reporting for GREGoR

Jupyter Notebook

awsbatch

json files and python scripts for managing AWS batch services

tagging_data_analysis

Analysis of tagging data exported from PIE

contactparser

An R package to parse and reformat the TOPMed website contacts table

WISG_2019

Course materials for WISG Module 4: Computational Pipeline for WGS Data, January 23-24, 2019

django-anvil-consortium-manager

Django app to manage AnVIL workspace permissions

SISG_2020