This is the development version of SimFFPE; for the stable release version, see SimFFPE.
NGS Read Simulator for FFPE TissueBioconductor version: Development (3.22)
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: 0000-0002-4281-8017
Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>
Citation (from within R, entercitation("SimFFPE")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SimFFPE")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SimFFPE")Follow Installation instructions to use this package in your R session.
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