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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.
| Version: | 2.1.6 |
| Depends: | R (≥ 3.5.0) |
| Imports: | stringr, dplyr, Biostrings, Rsamtools, GenomeInfoDb, BiocGenerics |
| Suggests: | BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 |
| Published: | 2024-08-25 |
| DOI: | 10.32614/CRAN.package.MicroSEC |
| 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 |
| Language: | en-US |
| Materials: | README NEWS |
| CRAN checks: | MicroSEC results |
| Reference manual: | MicroSEC.pdf |
| Vignettes: |
my-vignette (source, R code) |
| Package source: | MicroSEC_2.1.6.tar.gz |
| Windows binaries: | r-devel: MicroSEC_2.1.6.zip, r-release: MicroSEC_2.1.6.zip, r-oldrel: MicroSEC_2.1.6.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 |
| Old sources: | MicroSEC archive |
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These binaries (installable software) and packages are in development.
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