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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 expectancy, for each targeted sequenced tumor. For more details see Lee et al. (2024) <doi:10.1101/2023.05.18.23290188>.
| Version: | 1.0.4 |
| Depends: | R (≥ 4.1.0) |
| Imports: | stats, glmnet, GenomicRanges, IRanges, Biostrings, dplyr, BSgenome.Hsapiens.UCSC.hg19 |
| Suggests: | testthat |
| Published: | 2025-07-05 |
| DOI: | 10.32614/CRAN.package.SATS |
| Author: | DongHyuk Lee [aut], Bin Zhu [aut], Bill Wheeler [cre] |
| Maintainer: | Bill Wheeler <wheelerb at imsweb.com> |
| License: | GPL-2 |
| NeedsCompilation: | yes |
| CRAN checks: | SATS results |
| Reference manual: | SATS.html , SATS.pdf |
| Package source: | SATS_1.0.4.tar.gz |
| Windows binaries: | r-devel: SATS_1.0.4.zip, r-release: SATS_1.0.4.zip, r-oldrel: SATS_1.0.4.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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These binaries (installable software) and packages are in development.
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