Basic4Cseq

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("Basic4Cseq")

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

Documentation

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

Details

biocViews QualityControl, Software, Visualization
Version 1.0.2
In Bioconductor since BioC 2.14 (R-3.1)
License LGPL-3
Depends R (>= 3.0.0), Biostrings, ShortRead, caTools, GenomicRanges
Imports methods, RCircos, BSgenome.Ecoli.NCBI.20080805
Suggests BSgenome.Hsapiens.UCSC.hg19
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source Basic4Cseq_1.0.2.tar.gz
Windows Binary Basic4Cseq_1.0.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Basic4Cseq_1.0.2.tgz
Mac OS X 10.9 (Mavericks) Basic4Cseq_1.0.2.tgz
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