recipe bioconductor-txcutr

Transcriptome CUTteR






Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.

package bioconductor-txcutr

(downloads) docker_bioconductor-txcutr



depends bioconductor-annotationdbi:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-biostrings:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


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-txcutr

and update with::

   mamba update bioconductor-txcutr

To create a new environment, run:

mamba create --name myenvname bioconductor-txcutr

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

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