rSFFreader

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see rSFFreader.

rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers


Bioconductor version: 3.7

rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers into similar classes as are present for fastq files.

Author: Matt Settles <mattsettles at gmail.com>, Sam Hunter, Brice Sarver, Ilia Zhbannikov, Kyu-Chul Cho

Maintainer: Matt Settles <mattsettles at gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rSFFreader")

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

Details

biocViews DataImport, Sequencing, Software
Version 0.28.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends ShortRead(>= 1.23.17)
Imports methods, Biostrings, IRanges
System Requirements
URL
See More
Suggests xtable
Linking To S4Vectors(>= 0.13.8), IRanges, XVector, Biostrings
Enhances
Depends On Me
Imports Me hiReadsProcessor
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package rSFFreader_0.28.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) rSFFreader_0.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rSFFreader
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rSFFreader
Package Short Url https://bioconductor.org/packages/rSFFreader/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive