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/demultiplex.py) to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/FourCSeq.html

License

GPL (>= 3)

Recipe

/bioconductor-fourcseq/meta.yaml

Links

biotools: fourcseq

package bioconductor-fourcseq

(downloads) docker_bioconductor-fourcseq

Versions

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

>=2.42.0,<2.43.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-deseq2

>=1.22.0,<1.23.0

Depends bioconductor-genomicalignments

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-ggbio

>=1.30.0,<1.31.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-rtracklayer

>=1.42.0,<1.43.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-fda

Depends r-ggplot2

Depends r-gtools

Depends r-lsd

Depends r-matrix

Depends r-reshape2

Requirements

Installation

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 quay.io/biocontainers/bioconductor-fourcseq:<tag>

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