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acnviewer

Comprehensive genome-wide visualization of absolute copy number and copy neutral variations

atac-seq-pipeline

ENCODE ATAC-seq pipeline

bamdst

a lightweight bam file depth statistical tool

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

cellbender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

cinsignaturequantification

Quantifying copy number signatures from new copy number profiles

copynumber

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/copynumber.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=copynumber.

doabsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package

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ema

Fast & accurate alignment of barcoded short-reads

gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

gatk-qscripts

GATK QScripts used in our illumina variant calling pipeline.

gridss-purple-linx

Standalone GRIDSS/PURPLE/LINX pipeline

muse

Somatic point mutation caller

ngseasy

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

polysolver-singularity

Building a Singularity image of Polysolver

r-ici_mnb_survival

sigdriver

Driver discovery using mutational signatures

ts

Torrent Suite