Package: SATS
Title: Signature Analyzer for Targeted Sequencing (SATS)
Version: 1.0.11
Date: 2026-09-15
Authors@R: c(person(given="DongHyuk", family="Lee", role="aut", email="dhyuklee@pusan.ac.kr"),
             person(given="Bin", family="Zhu", role="aut", email="bin.zhu@nih.gov"),
             person(given="Bill", family="Wheeler", role="cre", email="wheelerb@imsweb.com"))
Description: Performs mutational signature analysis for tumors profiled
        by targeted sequencing. Unlike the canonical analysis of
        mutational signatures, SATS factorizes the mutation count
        matrix into a panel-context matrix (measuring the number of
        mutation opportunities per million base pairs for each tumor),
        a signature profile matrix, and a signature activity matrix.
        SATS also calculates the expected number of mutations
        attributed to each signature, namely the signature burden, for
        each tumor profiled by targeted sequencing. For more details
        see Lee et al. (2024) <doi:10.1101/2023.05.18.23290188>.
Imports: stats, glmnet, GenomicRanges, IRanges, Biostrings, dplyr
Depends: R (>= 4.1.0)
Suggests: testthat, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38
License: GPL-2
NeedsCompilation: yes
Packaged: 2026-10-16 06:13:33 UTC; root
Author: DongHyuk Lee [aut], Bin Zhu [aut], Bill Wheeler [cre]
Maintainer: Bill Wheeler <wheelerb@imsweb.com>
Config/pak/sysreqs: zlib1g-dev
Repository: https://wheelerb.r-universe.dev
Date/Publication: 2026-09-15 21:40:08 UTC
RemoteUrl: https://github.com/cran/SATS
RemoteRef: HEAD
RemoteSha: 14a63c031ef1965accbaa6506e32c62a1c254091