recipe bioconductor-phipdata

Container for PhIP-Seq Experiments






PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

package bioconductor-phipdata

(downloads) docker_bioconductor-phipdata



depends bioconductor-biocfilecache:


depends bioconductor-biocgenerics:


depends bioconductor-edger:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-cli:



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-phipdata

and update with::

   mamba update bioconductor-phipdata

To create a new environment, run:

mamba create --name myenvname bioconductor-phipdata

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-phipdata/tags`_ for valid values for ``<tag>``)

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