SimFFPE

DOI: 10.18129/B9.bioc.SimFFPE    

NGS Read Simulator for FFPE Tissue

Bioconductor version: Release (3.11)

This package simulates artifact chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissue.

Author: Lanying Wei

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	1.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	LGPL-3
Depends	Biostrings
Imports	dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods
LinkingTo
Suggests	BiocStyle
SystemRequirements
Enhances
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_1.0.0.tar.gz
Windows Binary	SimFFPE_1.0.0.zip
macOS 10.13 (High Sierra)	SimFFPE_1.0.0.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
Old Source Packages for BioC 3.11	Source Archive