recipe bioconductor-factr

Functional Annotation of Custom Transcriptomes






factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.

package bioconductor-factr

(downloads) docker_bioconductor-factr



depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-biostrings:


depends bioconductor-drawproteins:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-wiggleplotr:


depends r-base:


depends r-crayon:


depends r-data.table:


depends r-dplyr:


depends r-ggplot2:


depends r-pbapply:


depends r-purrr:


depends r-rcurl:


depends r-rlang:


depends r-stringr:


depends r-tibble:


depends r-tidyr:


depends r-xml:




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-factr

and update with::

   mamba update bioconductor-factr

To create a new environment, run:

mamba create --name myenvname bioconductor-factr

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

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