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 3.11 of Bioconductor; for the stable, up-to-date release version, see FourCSeq.

Package analyse 4C sequencing data

Bioconductor version: 3.11

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>

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

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 1.22.1
In Bioconductor since BioC 3.0 (R-3.1) (6 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_1.22.1.tar.gz
Windows Binary FourCSeq_1.22.1.zip
macOS 10.13 (High Sierra) FourCSeq_1.22.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/FourCSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FourCSeq
Package Short Url https://bioconductor.org/packages/FourCSeq/
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