Package: SATS
Title: Signature Analyzer for Targeted Sequencing (SATS)
Version: 1.0.6
Date: 2025-07-30
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 targeted sequenced tumors. Unlike the canonical analysis of mutational signatures, SATS factorizes the mutation counts matrix into a panel context matrix (measuring the size of the targeted sequenced genome for each tumor in the unit of million base pairs (Mb)), a signature profile matrix, and a signature activity matrix. SATS also calculates the expected number of mutations attributed by a signature, namely signature burden, for each targeted sequenced tumor. For more details see Lee et al. (2024) <doi:10.1101/2023.05.18.23290188>.
Imports: stats, glmnet, GenomicRanges, IRanges, Biostrings, dplyr,
        BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38
Depends: R (>= 4.1.0)
Suggests: testthat
License: GPL-2
NeedsCompilation: yes
Packaged: 2025-07-31 17:07:29 UTC; wheelerwi
Author: DongHyuk Lee [aut],
  Bin Zhu [aut],
  Bill Wheeler [cre]
Maintainer: Bill Wheeler <wheelerb@imsweb.com>
Repository: CRAN
Date/Publication: 2025-08-18 12:40:02 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2026-02-04 04:04:33 UTC; windows
Archs: x64
