Pinned Repositories
banovichlab
Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).
bisbee
alternative splicing analysis pipeline
CovGen
Creates a target specific exome_full192.coverage.txt file required by MutSig
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
jetstream_resources
Collection of scripts and README files tracking the source and generation of reference genomes and annotation files
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.
MMRF_CoMMpass
A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.
phoenix
Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
vcfMerger2
Dynamic vcfMerger for 2 to N somatic variants vcf files
Translational Genomics Research Institute's Repositories
tgen/banovichlab
Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).
tgen/CovGen
Creates a target specific exome_full192.coverage.txt file required by MutSig
tgen/MMRF_CoMMpass
A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.
tgen/bisbee
alternative splicing analysis pipeline
tgen/phoenix
Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
tgen/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
tgen/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.
tgen/vcfMerger2
Dynamic vcfMerger for 2 to N somatic variants vcf files
tgen/Institutional_Instructions
Description of institutional rules and regulations regarding the usage of github, plus usage guidelines
tgen/jetstream_resources
Collection of scripts and README files tracking the source and generation of reference genomes and annotation files
tgen/ppmi-qc-wt-paper
QC of whole blood whole transcriptome for PPMI
tgen/gvm
Replacement for LumosVar preprocess step
tgen/ppmi-rnaseq-wb-paper
code used to generate figures for the ppmi whole blood rnaseq paper
tgen/coyote
tgen/GemDb
GemDb mongo variants/annotations hub
tgen/pegasusPipe
tgen/Post_Medusa_Processing
tgen/tempe
A container focused and streamlined iteration of the Phoenix pipeline
tgen/MARS
Check the purity of a multiple myeloma tumor sample with this tool.
tgen/snpSniffer
Tool for checking genotype concordance between multiple assays
tgen/containers
tgen/docker_factory
Create docker images from scratch
tgen/GemDb37
Variant database for human genome build 37, includes public annotations and various TGen projects.
tgen/GemDb38
tgen/gencode-plus-lncipedia
non-redundant genome annotation combining GENCODE 29 and lncipedia 5.2
tgen/ichorCNA
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
tgen/jetstream_containers
Containers for running TGen Jetstream pipelines
tgen/Keats_Lab_Public
Public resources from the Keats Lab at TGen
tgen/manta
Structural variant and indel caller for mapped sequencing data
tgen/tgen-jetstream-docs