SimFFPE

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SimFFPE.

NGS Read Simulator for FFPE Tissue


Bioconductor version: 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>

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

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

Details

biocViews Alignment, DataImport, MultipleComparison, SequenceMatching, Sequencing, Software
Version 1.12.0
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
See More
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_1.12.0.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