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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rSFFreader")
In most cases, you don't need to download the package archive at all.
rSFFreader
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
Bioconductor version: 2.14
rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers. The plan is to also write out sff files and to read in flowgrams with some utils
Author: Matt Settles <msettles at uidaho.edu>, Sam Hunter, Brice Sarver, Ilia Zhbannikov, Kyu-Chul Cho
Maintainer: Matt Settles <msettles at uidaho.edu>
Citation (from within R,
enter citation("rSFFreader")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rSFFreader")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rSFFreader")
| R Script | An introduction to rSFFreader | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Sequencing, Software |
| Version | 0.12.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.13.0), BiocGenerics, IRanges(>= 1.21.10), XVector(>= 0.3.2), Biostrings(>= 2.31.3), GenomicRanges, ShortRead(>= 1.15.9), xtable, methods |
| Imports | methods, IRanges, XVector, Biostrings, ShortRead, GenomicRanges, Biobase |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rSFFreader_0.12.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | rSFFreader_0.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | rSFFreader_0.12.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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