To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ReQON")
In most cases, you don't need to download the package archive at all.
ReQON
Recalibrating Quality Of Nucleotides
Bioconductor version: 3.0
Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.
Author: Christopher Cabanski, Keary Cavin, Chris Bizon
Maintainer: Christopher Cabanski <ccabansk at genome.wustl.edu>
Citation (from within R,
enter citation("ReQON")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ReQON")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ReQON")
| R Script | ReQON Tutorial | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Preprocessing, QualityControl, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL-2 |
| Depends | R (>= 3.0.2), Rsamtools, seqbias |
| Imports | rJava, graphics, stats, utils, grDevices |
| LinkingTo | |
| Suggests | BiocStyle |
| SystemRequirements | Java version >= 1.6 |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ReQON_1.12.0.tar.gz |
| Windows Binary | ReQON_1.12.0.zip |
| Mac OS X 10.6 (Snow Leopard) | ReQON_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | ReQON_1.12.0.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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