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SimFFPE
This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see SimFFPE.
NGS Read Simulator for FFPE Tissue
Bioconductor version: 3.21
The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.
Author: Lanying Wei [aut, cre] ORCID iD ORCID: 0000-0002-4281-8017
Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>
citation("SimFFPE")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SimFFPE")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SimFFPE")
Details
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Follow Installation instructions to use this package in your R session.