SimFFPE

DOI: 10.18129/B9.bioc.SimFFPE    

This is the development version of SimFFPE; for the stable release version, see SimFFPE.

NGS Read Simulator for FFPE Tissue

Bioconductor version: Development (3.15)

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 <lanying.wei at uni-muenster.de>

Maintainer: <>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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.

Documentation

PDF   Reference Manual

Details

biocViews Alignment, DataImport, MultipleComparison, SequenceMatching, Sequencing, Software
Version 1.7.0
In Bioconductor since BioC 3.11 (R-4.0) (1.5 years)
License LGPL-3
Depends Biostrings
Imports dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods
LinkingTo
Suggests BiocStyle
SystemRequirements
Enhances
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Depends On Me
Imports Me
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Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/SimFFPE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SimFFPE
Package Short Url https://bioconductor.org/packages/SimFFPE/
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