To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Basic4Cseq")

In most cases, you don't need to download the package archive at all.

Basic4Cseq

   

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see Basic4Cseq.

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Bioconductor version: 3.1

Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Author: Carolin Walter

Maintainer: Carolin Walter <carolin.walter at uni-muenster.de>

Citation (from within R, enter citation("Basic4Cseq")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Basic4Cseq")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Basic4Cseq")

 

PDF R Script Basic4Cseq: an R/Bioconductor package for the analysis of 4C-seq data
PDF   Reference Manual

Details

biocViews QualityControl, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 2.14 (R-3.1) (2 years)
License LGPL-3
Depends R (>= 3.0.0), Biostrings, ShortRead, caTools, GenomicRanges
Imports methods, RCircos, BSgenome.Ecoli.NCBI.20080805
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19
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 Basic4Cseq_1.4.0.tar.gz
Windows Binary Basic4Cseq_1.4.0.zip
Mac OS X 10.6 (Snow Leopard) Basic4Cseq_1.4.0.tgz
Mac OS X 10.9 (Mavericks) Basic4Cseq_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Basic4Cseq/tree/release-3.1
Package Short Url http://bioconductor.org/packages/Basic4Cseq/
Package Downloads Report Download Stats

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