DESCRIPTION

Package: superFreq
Title: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.
Version: 1.6
Authors@R: person("Christoffer", "Flensburg", email = "flensburg.c@wehi.edu.au", role = c("aut", "cre"))
Description: SuperFreq analyses SNVs and CNAs of multiple cancer exomes, sharing
    all information across samples and mutation types. The inputs are the bam-files
    and a preliminary SNV calling in .vcf format. SuperFreq filters and annotates
    the SNVs, calls CNAs and tracks clones over samples from the same individual.
    A matched normal improves results, but is not necessary. SuperFreq requireas at
    least two (preferably 5-10 or more) reference normal samples that do not have to
    be related to the studied cancer samples, but must be from the same sequencing
    platform and capture. These are used to improve results through variance of read
    depth and requrring false SNVs amongst other things. SuperFreq produces ample
    output in terms of plots and spread sheets, both for identifying properties of
    the cancer samples and for quality control.
biocViews:
Depends:
    R (>= 4.4), WriteXLS (>= 4.0), BiocGenerics (>= 0.26), GenomicRanges (>= 1.32.7), IRanges (>= 2.14.12), S4Vectors (>= 0.18.3), biomaRt (>= 2.36.1), Rsamtools (>= 1.32.3), R.oo (>= 1.22), Rsubread (>= 1.30.9), limma (>= 3.36.5), parallel, MutationalPatterns (>= 1.6.1), BSgenome.Mmusculus.UCSC.mm10 (>= 1.4.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1)
License: MIT
LazyData: true
RoxygenNote: 7.3.1