SimFFPE

This is the released version of SimFFPE; for the devel version, see SimFFPE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

NGS Read Simulator for FFPE Tissue

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-4281-8017

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

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

Lanying Wei. SimFFPE: NGS Read Simulator for FFPE Tissue. doi:10.18129/B9.bioc.SimFFPE, R package version 1.24.0, https://bioconductor.org/packages/SimFFPE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	LGPL-3
Depends	Biostrings
Imports	dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods
System Requirements
URL

Suggests	BiocStyle
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	SimFFPE_1.24.0.tar.gz
Windows Binary (x86_64)	SimFFPE_1.24.0.zip
macOS Binary (big-sur-x86_64)	SimFFPE_1.24.0.tgz
macOS Binary (sonoma-arm64)	SimFFPE_1.24.0.tgz
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/
Package Downloads Report	Download Stats