SimFFPE

DOI: 10.18129/B9.bioc.SimFFPE    

This is the development version of SimFFPE; to use it, please install the devel version of Bioconductor.

NGS Read Simulator for FFPE Tissue

Bioconductor version: Development (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>

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

Installation

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

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 0.99.32
In Bioconductor since BioC 3.11 (R-4.0)
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_0.99.32.tar.gz
Windows Binary SimFFPE_0.99.32.zip
Mac OS X 10.11 (El Capitan)
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

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