FourCSeq

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see FourCSeq.

Package analyse 4C sequencing data

Bioconductor version: 3.10

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 <daggoth at gmx.de>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FourCSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("FourCSeq")

FourCSeq	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Preprocessing, Sequencing, Software
Version	1.20.0
In Bioconductor since	BioC 3.0 (R-3.1) (9.5 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
System Requirements
URL

Suggests	BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	FourCSeq_1.20.0.tar.gz
Windows Binary	FourCSeq_1.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	FourCSeq_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FourCSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FourCSeq
Bioc Package Browser	https://code.bioconductor.org/browse/FourCSeq/
Package Short Url	https://bioconductor.org/packages/FourCSeq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.10	Source Archive