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 |
| Reference manual: | MicroSEC.pdf |
| Vignettes: |
my-vignette |
| 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: MicroSEC_1.1.3.tgz, r-oldrel: not available |
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