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
devtools::install_github("VanLoo-lab/ASCAT.sc", build_opts = c("--no-build-vignettes"))Make sure to install dependencies before installing (this might take a while):
devtools::install_github("iovlaicu/copynumber")
BiocManager::install(c("GenomicRanges", "Biostrings", "DNAcopy",
"minfi", "conumee", "Rsamtools", "xgboost"))The methylation mode now depends on pre-compiled bad probes, and panel of normal diploid data for 450K, Epicv1 (~0.5GB) and Epicv2 arrays, which are in the R data package ASCAT.scDataMeth.
As the files are big and github bandwidth is limited, you can download the package as a zip file here and build/install for R as follows:
R CMD build ASCAT.scDataMeth
R CMD install ASCAT.scDataMeth_0.1.tar.gz
For Epicv2, also install the manifest and annotations:
BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2manifest")
BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")Go to Wiki pages.
Vignettes are now obsolete, but remain a good way to understand the different steps of the pipelines.
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