seqbias

Estimation of per-position bias in high-throughput sequencing data

Bioconductor version: Development (3.0)

This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

Author: Daniel Jones <dcjones at cs.washington.edu>

Maintainer: Daniel Jones <dcjones at cs.washington.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("seqbias")

To cite this package in a publication, start R and enter:

    citation("seqbias")

Documentation

PDF R Script Assessing and Adjusting for Technical Bias in High Throughput Sequencing Data
PDF   Reference Manual

Details

biocViews Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 2.8 (R-2.13)
License LGPL-3
Depends R (>= 2.13.0), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0), methods
Imports zlibbioc
Suggests Rsamtools, ggplot2
System Requirements
URL
Depends On Me ReQON
Imports Me
Suggests Me

Package Downloads

Package Source seqbias_1.13.0.tar.gz
Windows Binary seqbias_1.13.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) seqbias_1.13.0.tgz
Mac OS X 10.9 (Mavericks)
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