SimFFPE

DOI: 10.18129/B9.bioc.SimFFPE  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SimFFPE.

NGS Read Simulator for FFPE Tissue

Bioconductor version: 3.16

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 "4.2") 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	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 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
Links To Me
Build Report

Package Archives

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

Source Package	SimFFPE_1.10.0.tar.gz
Windows Binary	SimFFPE_1.10.0.zip (64-bit only)
macOS Binary (x86_64)	SimFFPE_1.10.0.tgz
macOS Binary (arm64)	SimFFPE_1.10.0.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