recipe bioconductor-fourcseq

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.



GPL (>= 3)




biotools: fourcseq

package bioconductor-fourcseq

(downloads) docker_bioconductor-fourcseq


1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.4.0-1, 1.4.0-0

Depends bioconductor-biobase


Depends bioconductor-biostrings


Depends bioconductor-deseq2


Depends bioconductor-genomicalignments


Depends bioconductor-genomicranges


Depends bioconductor-ggbio


Depends bioconductor-rsamtools


Depends bioconductor-rtracklayer


Depends bioconductor-summarizedexperiment


Depends r-base


Depends r-fda

Depends r-ggplot2

Depends r-gtools

Depends r-lsd

Depends r-matrix

Depends r-reshape2



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-fourcseq

and update with:

conda update bioconductor-fourcseq

or use the docker container:

docker pull<tag>

(see bioconductor-fourcseq/tags for valid values for <tag>)