seqbias

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

Bioconductor version: 2.8

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, HighThroughputSequencing
Depends R (>= 2.13.0), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0), methods
Imports
Suggests
System Requirements
License LGPL-3
URL
Depends On Me
Imports Me
Suggests Me
Version 1.0.0
Since Bioconductor 2.8 (R-2.13)

Package Downloads

Package Source seqbias_1.0.0.tar.gz
Windows Binary seqbias_1.0.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary seqbias_1.0.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center