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R package with supporting routines for the SCAN2 pipeline. These routines may not be particularly useful when separate from the main pipeline.

See https://github.com/parklab/SCAN2 for the full pipeline.

Major caveat

This package requires command line access to a Linux system. There are 3 reasons:

  1. Custom tabix parsing to read in large files. This uses a command line tabix executable piped into the *nix cut command. Sometimes tabix is replaced by a simple gunzip -c when no genomic region is given.
  2. The bedtoolsr package: this is a wrapper around bedtools executables.
  3. The SigProfilerMatrixGeneratorR package: another wrapper (via the R R<->python reticulate interface) to a python library.

Extra installation steps

After installing r-scan2, the user must download and install a reference genome for SigProfilerMatrixGenerator. See the SCAN2 pipeline README for detailed instructions.