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battenberg

Battenberg R package for subclonal copynumber estimation

battenberg_chry_snps

Script to create Y chromosome SNPs for Battenberg

battenberg_logr_totalcn

Estimate total copy number from logR data

battenberg_templates

Battenberg output templates

clonality_management

copykat_pipeline

copynumber

Bioconductor copynumber package with hg38 and mm10

dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

dpclust

Dirichlet Process based methods for subclonal reconstruction of tumours

dpclust3p

Dirichlet Process Clustering Pre-Processing Pipeline

generate_icgc_batch_overview

icgc_consensus_clustering_assignment

ICGC PCAWG-11 pipeline used for assignment of SNVs, Indels and SVs to consensus mutation clusters

icgc_consensus_copynumber

ICGC PCAWG-11 consensus copy number pipeline

icgc_consensus_purity

icgc_copynumber_event_inventory

Code to create a copynumber event inventory for ICGC PCAWG

icgc_pcawg11_calibration

ICGC PCAWG-11 Calibration code for subclonal architecture

icgc_resolve_wgd

icgc_summary_table

icgcconsensuscn_to_bb

Parser for ICGC consensus CN to Battenberg format

modern-unix

A collection of modern/faster/saner alternatives to common unix commands.

mutationtime.r

An R script to time somatic mutations

nextflow_allelecounter

Nextflow implementation of the alleleCounter tool

qdnaseq

QDNAseq package for Bioconductor

qdnaseq_pipeline

randomclone

Establish random subclonal reconstructions from mutation data

randomclone_smchet_docker

RandomClone Single SMC-het pipeline

replication_summarise

Code to summarise replication timing data

sccna

R package for logR-based copy number profiling for shallow coverage/single cell (SC) experiments

smchet_utils

Functions for SMC-het pipelines

targeted_het_snp_imbalance

Pipeline to call significant imbalance of heterozygous SNPs