MicroSEC: Sequence Error Filtering Pipeline for FFPE Samples

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.

Version: 1.1.3
Depends: R (≥ 3.4.0)
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
Published: 2020-12-02
Author: Masachika Ikegami [aut, cre]
Maintainer: Masachika Ikegami <ikegamitky at gmail.com>
BugReports: https://github.com/MANO-B/MicroSEC/issues
License: MIT + file LICENSE
URL: https://github.com/MANO-B/MicroSEC/
NeedsCompilation: no
Materials: README
CRAN checks: MicroSEC results

Documentation:

Reference manual: MicroSEC.pdf
Vignettes: my-vignette

Downloads:

Package source: MicroSEC_1.1.3.tar.gz
Windows binaries: r-devel: MicroSEC_1.1.3.zip, r-release: MicroSEC_1.1.3.zip, r-oldrel: MicroSEC_1.1.3.zip
macOS binaries: r-release (arm64): MicroSEC_1.1.3.tgz, r-release (x86_64): MicroSEC_1.1.3.tgz, r-oldrel: MicroSEC_1.1.3.tgz

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