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source("http://bioconductor.org/biocLite.R")
biocLite("seqbias")
In most cases, you don't need to download the package archive at all.
seqbias
Estimation of per-position bias in high-throughput sequencing data
Bioconductor version: 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>
Citation (from within R,
enter citation("seqbias")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("seqbias")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("seqbias")
| R Script | Assessing and Adjusting for Technical Bias in High Throughput Sequencing Data | |
| Reference Manual |
Details
| biocViews | Sequencing, Software |
| Version | 1.14.0 |
| 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 |
| LinkingTo | Rsamtools |
| Suggests | Rsamtools, ggplot2 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | ReQON |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | seqbias_1.14.0.tar.gz |
| Windows Binary | seqbias_1.14.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | seqbias_1.14.0.tgz |
| Mac OS X 10.9 (Mavericks) | seqbias_1.14.0.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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