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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 MutSigMMRF_CoMMpass
A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.bisbee
alternative splicing analysis pipelinephoenix
Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38jetstream
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 schedulersLumosVar
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 filestCoNuT
TGen Copy Number Tooljetstream_resources
Collection of scripts and README files tracking the source and generation of reference genomes and annotation filesgvm
Replacement for LumosVar preprocess stepppmi-qc-wt-paper
QC of whole blood whole transcriptome for PPMIppmi-rnaseq-wb-paper
code used to generate figures for the ppmi whole blood rnaseq paperPost_Medusa_Processing
pegasusPipe
tempe
A container focused and streamlined iteration of the Phoenix pipelineseurat
Tumor-Normal Variant Callercoyote
medusaPipe
GemDb
GemDb mongo variants/annotations hubNeoantigen-pred
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