SimFFPE

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see SimFFPE.

NGS Read Simulator for FFPE Tissue

Bioconductor version: 3.14

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>

Citation (from within R, enter citation("SimFFPE")):

Installation

To install this package, start R (version "4.1") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, DataImport, MultipleComparison, SequenceMatching, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (4 years)
License	LGPL-3
Depends	Biostrings
Imports	dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods
System Requirements
URL

Suggests	BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SimFFPE_1.6.0.tar.gz
Windows Binary	SimFFPE_1.6.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	SimFFPE_1.6.0.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 3.14	Source Archive