Package: MicroSEC
Title: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded
        Samples
Version: 2.1.3
Maintainer: Masachika Ikegami <ikegamitky@gmail.com>
Authors@R: 
    person(given = "Masachika",
           family = "Ikegami",
           role = c("aut", "cre"),
           email = "ikegamitky@gmail.com")
Description: Clinical sequencing of tumor is usually performed on formalin-fixed
    and paraffin-embedded samples and have many sequencing errors. We found that
    the majority of these errors are detected in chimeric read caused by
    single-strand DNA with micro-homology. Our filtering pipeline focuses on the
    uneven distribution of the artifacts in each read and removes such errors in
    formalin-fixed and paraffin-embedded samples without over-eliminating the
    true mutations detected in fresh frozen samples.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
Depends: R (>= 3.5.0)
RoxygenNote: 7.3.1
LazyData: true
Imports: stringr, dplyr, Biostrings, Rsamtools, GenomeInfoDb,
        BiocGenerics
Suggests: BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
        BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
VignetteBuilder: knitr
URL: https://github.com/MANO-B/MicroSEC/
BugReports: https://github.com/MANO-B/MicroSEC/issues
NeedsCompilation: no
Packaged: 2024-07-26 10:14:23 UTC; ikegami
Author: Masachika Ikegami [aut, cre]
Repository: CRAN
Date/Publication: 2024-07-26 15:00:06 UTC
