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.
|License||GPL (>= 3)|
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-fourcseq
and update with:
conda update bioconductor-fourcseq
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-fourcseq.