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Singer Ma's Projects

bcftools icon bcftools

This is the official development repository for BCFtools. To compile, the bcftools+calling branch of htslib is needed: git clone --branch=bcftools+calling git://github.com/samtools/htslib.git htslib

cgdata icon cgdata

Python API to work with the cgData standard

cramtools icon cramtools

Format specification and java implementation for next-gen data.

dx-ccle-fpkm icon dx-ccle-fpkm

DNAnexus platform applets to calculate expression levels from CCLE RNA-Seq data

gatk icon gatk

GATK Changes for TCGA Repository

gatk-1 icon gatk-1

Official code repository for GATK versions 4 and up

rnaseq_tutorial icon rnaseq_tutorial

An educational tutorial and working demonstration pipeline for RNA-seq analysis including an introduction to: cloud computing, next generation sequence file formats, reference genomes, gene annotation, expression analysis, differential expression analysis, alternative splicing analysis, data visualization, and interpretation.

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