Stefan Dentro's repositories
icgc_consensus_copynumber
ICGC PCAWG-11 consensus copy number pipeline
randomclone
Establish random subclonal reconstructions from mutation data
icgc_copynumber_event_inventory
Code to create a copynumber event inventory for ICGC PCAWG
icgcConsensusCN_to_BB
Parser for ICGC consensus CN to Battenberg format
targeted_het_snp_imbalance
Pipeline to call significant imbalance of heterozygous SNPs
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
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
icgc_consensus_clustering_assignment
ICGC PCAWG-11 pipeline used for assignment of SNVs, Indels and SVs to consensus mutation clusters
icgc_pcawg11_calibration
ICGC PCAWG-11 Calibration code for subclonal architecture
MutationTime.R
An R script to time somatic mutations
QDNAseq
QDNAseq package for Bioconductor
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
TidyTuesday
📊 My contributions to the #TidyTuesday challenge