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>

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

Installation

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

Details

biocViews Preprocessing, Sequencing, Software
Version 1.24.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
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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 git@git.bioconductor.org:packages/FourCSeq
Package Short Url https://bioconductor.org/packages/FourCSeq/
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Old Source Packages for BioC 3.12 Source Archive