FourCSeq

DOI: 10.18129/B9.bioc.FourCSeq    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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 [aut], Mike Smith [cre]

Maintainer: Mike Smith <mike.smith at embl.de>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	FourCSeq
PDF		Reference Manual

Details

biocViews	Preprocessing, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 3.0 (R-3.1) (6.5 years)
License	GPL (>= 3)
Depends	R (>= 3.0), splines, LSD, DESeq2(>= 1.9.11), ggplot2
Imports	Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix, methods
LinkingTo
Suggests	BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	FourCSeq_1.24.0.tar.gz
Windows Binary	FourCSeq_1.24.0.zip
macOS 10.13 (High Sierra)	FourCSeq_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FourCSeq
Source Repository (Developer Access)	git clone [email protected]:packages/FourCSeq
Package Short Url	https://bioconductor.org/packages/FourCSeq/
Package Downloads Report	Download Stats