tgen/ppmi-qc-wt-paper

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Created about 4 years ago
Updated about 4 years ago

tgen/ppmi-qc-wt-paper

tgen

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QC of whole blood whole transcriptome for PPMI

banovichlab

Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).

CovGen

Creates a target specific exome_full192.coverage.txt file required by MutSig

MMRF_CoMMpass

A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.

bisbee

alternative splicing analysis pipeline

phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38

jetstream

Workflow management system written as a pure Python package and command-line utility. It supports complex workflows modeled as directed- acyclic graphs (DAGs), and execution on batch schedulers

LumosVar

lumosVar2

Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.

vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files

tCoNuT

TGen Copy Number Tool

Institutional_Instructions

Description of institutional rules and regulations regarding the usage of github, plus usage guidelines

jetstream_resources

Collection of scripts and README files tracking the source and generation of reference genomes and annotation files

gvm

Replacement for LumosVar preprocess step

ppmi-rnaseq-wb-paper

code used to generate figures for the ppmi whole blood rnaseq paper

Post_Medusa_Processing

pegasusPipe

tempe

A container focused and streamlined iteration of the Phoenix pipeline

seurat

Tumor-Normal Variant Caller

coyote

medusaPipe

GemDb

GemDb mongo variants/annotations hub

Neoantigen-pred