seqbias

DOI: 10.18129/B9.bioc.seqbias    

This is the development version of seqbias; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("seqbias")

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("seqbias")

 

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

Details

biocViews Sequencing, Software
Version 1.33.1
In Bioconductor since BioC 2.8 (R-2.13) (8.5 years)
License LGPL-3
Depends R (>= 3.0.2), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0), methods
Imports
LinkingTo Rhtslib(>= 1.15.3)
Suggests Rsamtools, ggplot2
SystemRequirements GNU make
Enhances
URL
Depends On Me ReQON
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package seqbias_1.33.1.tar.gz
Windows Binary seqbias_1.33.0.zip
Mac OS X 10.11 (El Capitan) seqbias_1.33.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/seqbias
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seqbias
Package Short Url https://bioconductor.org/packages/seqbias/
Package Downloads Report Download Stats

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