To install this package, start R and enter:

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

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

FourCSeq

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see FourCSeq.

Package analyse 4C sequencing data

Bioconductor version: 3.2

FourCSeq is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. The package provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script (extdata/python/demultiplex.py) to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.

Author: Felix A. Klein, EMBL Heidelberg

Maintainer: Felix A. Klein <felix.klein at embl.de>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("FourCSeq")

PDF		FourCSeq
PDF		Reference Manual

Details

biocViews	Preprocessing, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.0 (R-3.1) (1.5 years)
License	GPL (>= 3)
Depends	R (>= 3.0), GenomicRanges, ggplot2, DESeq2(>= 1.9.11), splines, methods, LSD
Imports	DESeq2, Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix
LinkingTo
Suggests	BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene
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	FourCSeq_1.4.0.tar.gz
Windows Binary	FourCSeq_1.4.0.zip
Mac OS X 10.6 (Snow Leopard)	FourCSeq_1.4.0.tgz
Mac OS X 10.9 (Mavericks)	FourCSeq_1.4.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/FourCSeq/tree/release-3.2
Package Short Url	http://bioconductor.org/packages/FourCSeq/
Package Downloads Report	Download Stats

Documentation »

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