To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("FourCSeq")

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

FourCSeq

DOI: 10.18129/B9.bioc.FourCSeq    

This is the development version of FourCSeq; for the stable release version, see FourCSeq.

Package analyse 4C sequencing data

Bioconductor version: Development (3.6)

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("http://bioc.ism.ac.jp/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 R Script FourCSeq
PDF   Reference Manual

Details

biocViews Preprocessing, Sequencing, Software
Version 1.11.1
In Bioconductor since BioC 3.0 (R-3.1) (3 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.

Source Package FourCSeq_1.11.1.tar.gz
Windows Binary FourCSeq_1.11.1.zip
Mac OS X 10.11 (El Capitan) FourCSeq_1.11.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/FourCSeq
Package Short Url http://bioconductor.org/packages/FourCSeq/
Package Downloads Report Download Stats

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