Copy number from DNA profiling techniques, including single-cell (sc), shallow-coverage (sc), and targeted sequencing, as well as methylation arrays
First download the zip file on disk and then build and install with the following commands
R CMD BUILD --no-build-vignettes ASCAT.sc/
R CMD INSTALL ASCAT.sc_1.0.tar.gz
R CMD build --no-build-vignettes ASCAT.sc/
R CMD install ASCAT.sc_0.1.tar.gz
Alternatively, you can install with devtools in an R session:
devtools::install_github("VanLoo-lab/ASCAT.sc", build_opts = c("--no-build-vignettes"))
The methylation mode now depends on pre-compiled bad loci and panel of normal data for 450K and Epicv1 arrays (~0.5GB), which are in the R data package ASCAT.scDataMeth:
devtools::install_github("galder-max/ASCAT.scDataMeth")
As the files are big, you might want to download the package (https://github.com/galder-max/ASCAT.scDataMeth) as a zip file and install from R:
R CMD build ASCAT.scDataMeth
R CMD install ASCAT.scDataMeth_0.1.tar.gz
Make sure to install dependencies before installing (this might take a while):
BiocManager::install(c("GenomicRanges", "Biostrings", "DNAcopy", "minfi", "conumee", "Rsamtools", "xgboost"))
See vignettes for how-to pipelines.
ASCAT.sc total copy-number profiles on cell lines from various sources (GDSC and CCLE) can be found here: https://drive.google.com/drive/folders/1RwhF9cw6KP55fHtlNKTzk36syXN9fspo?usp=sharing 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