recipe bioconductor-basic4cseq

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data







biotools: basic4cseq, doi: 10.1093/bioinformatics/btu497

Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

package bioconductor-basic4cseq

(downloads) docker_bioconductor-basic4cseq



depends bioconductor-biostrings:


depends bioconductor-bsgenome.ecoli.ncbi.20080805:


depends bioconductor-genomicalignments:


depends bioconductor-genomicranges:


depends r-base:


depends r-catools:

depends r-rcircos:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-basic4cseq

and update with::

   mamba update bioconductor-basic4cseq

To create a new environment, run:

mamba create --name myenvname bioconductor-basic4cseq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-basic4cseq/tags`_ for valid values for ``<tag>``)

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