Package: MicroSEC
Title: Sequence Error Filtering Pipeline for FFPE Samples
Version: 1.1.3
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 (FFPE) 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 microhomology. Our filtering pipeline
    focuses on the uneven distribution of the artifacts in each read and removes
    such errors in FFPE samples without over-eliminating the true mutations
    detected in fresh frozen samples.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
RoxygenNote: 7.1.1
Imports: tidyr, openxlsx, data.table, R.utils, stringr, magrittr,
        dplyr, gtools, Biostrings, GenomicAlignments, Rsamtools,
        GenomeInfoDb, BiocGenerics
Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Mmusculus.UCSC.mm10, knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/MANO-B/MicroSEC/
BugReports: https://github.com/MANO-B/MicroSEC/issues
NeedsCompilation: no
Packaged: 2020-11-30 11:40:59 UTC; ikegami
Author: Masachika Ikegami [aut, cre]
Maintainer: Masachika Ikegami <ikegamitky@gmail.com>
Repository: CRAN
Date/Publication: 2020-12-02 10:30:07 UTC
Built: R 4.0.2; ; 2020-12-03 11:49:06 UTC; unix
