SimFFPE

DOI: 10.18129/B9.bioc.SimFFPE  

NGS Read Simulator for FFPE Tissue

Bioconductor version: Release (3.17)

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]

Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>

Installation

To install this package, start R (version "4.3") 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")

 

PDF	R Script	An introduction to SimFFPE
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, DataImport, MultipleComparison, SequenceMatching, Sequencing, Software
Version	1.12.0
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	LGPL-3
Depends	Biostrings
Imports	dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SimFFPE_1.12.0.tar.gz
Windows Binary	SimFFPE_1.12.0.zip
macOS Binary (x86_64)	SimFFPE_1.12.0.tgz
macOS Binary (arm64)	SimFFPE_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SimFFPE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SimFFPE
Bioc Package Browser	https://code.bioconductor.org/browse/SimFFPE/
Package Short Url	https://bioconductor.org/packages/SimFFPE/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive