MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples

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

Documentation:

Reference manual:	MicroSEC.pdf
Vignettes:	my-vignette (source, R code)

Downloads:

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

Linking:

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