ASCAT.sc

Copy number from DNA profiling techniques, including single-cell (sc), shallow-coverage (sc), and targeted sequencing, as well as methylation arrays

Install

You can install from github with the following command:

devtools::install_github("VanLoo-lab/ASCAT.sc", build_opts = c("--no-build-vignettes"))

Dependencies

Make sure to install dependencies before installing (this might take a while):

devtools::install_github("iovlaicu/copynumber")
BiocManager::install(c("GenomicRanges", "Biostrings", "DNAcopy", "Rsamtools", "xgboost"))

Examples and Usage

Go to Wiki pages.

Vignettes are now obsolete, but remain a good way to understand the different steps of the pipelines.

Cell-line profiles

ASCAT.sc total copy-number profiles on cell lines from various sources (GDSC and CCLE) can be found here. These are accompanied by the R script to derive the profiles, as well as sample ID mapping and QC flags.

Credits to: Philip S Smith, CRUK Cambridge Institute

See also

ASCAT.ma is a separate package, that is built in ASCAT.sc' framework to derive genomewide copy-number calls, purity and ploidy estimates from (Illumina) methylation arrays.