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/ 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>

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


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PDF R Script FourCSeq
PDF   Reference Manual


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
Suggests BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene
Depends On Me
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