To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DNaseR")
In most cases, you don't need to download the package archive at all.
DNaseR
DNase I footprinting analysis of DNase-seq data
Bioconductor version: 3.0
Strand-specific digital genomic footprinting in 'double-hit' DNase-seq data. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized count differences of opposed sign at each DNA strand. This is done in order to determine the protein-binding footprint flanks. Preprocessing of the mapped reads is recommended before running DNaseR (e.g., quality checking and removal of sequence-specific biases).
Author: Pedro Madrigal <pm12 at sanger.ac.uk>
Maintainer: Pedro Madrigal <pm12 at sanger.ac.uk>
Citation (from within R,
enter citation("DNaseR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DNaseR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DNaseR")
| R Script | DNaseR Vignette | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Genetics, Software, Transcription |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-2 + file LICENSE |
| Depends | R (>= 2.10.0), BiocGenerics, S4Vectors, IRanges |
| Imports | GenomeInfoDb, GenomicRanges, Rsamtools |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics |
| SystemRequirements | |
| 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 | DNaseR_1.4.0.tar.gz |
| Windows Binary | DNaseR_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | DNaseR_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | DNaseR_1.4.0.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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