recipe bioconductor-tximport

Import and summarize transcript-level estimates for transcript- and gene-level analysis



LGPL (>=2)




biotools: tximport

Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

package bioconductor-tximport

(downloads) docker_bioconductor-tximport



depends r-base:




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-tximport

and update with::

   mamba update bioconductor-tximport

To create a new environment, run:

mamba create --name myenvname bioconductor-tximport

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

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