recipe r-txrevise

Construct custom transcript annotations for Salmon and kallisto

Homepage:

https://github.com/kauralasoo/txrevise

License:

Apache / Apache 2.0

Recipe:

/r-txrevise/meta.yaml

Links:

doi: 10.7554/eLife.41673

txrevise R package provides utilites to pre-process Ensembl transcript annotations to quantify differences in transcript strucuture (alternative promoters, alternative splicing, alternative poly-adenylation) either between experimental conditions or genotypes (e.g. for transcript usage quntitative trait loci (tuQTL) mapping).

package r-txrevise

(downloads) docker_r-txrevise

versions:

2.0-2,  2.0-1,  2.0-0,  0.1-3,  0.1-2,  0.1-1,  0.1-0

depends bioconductor-genomicfeatures:

depends bioconductor-genomicranges:

depends bioconductor-iranges:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-purrr:

depends r-purrrlyr:

depends r-readr:

depends r-tidyr:

requirements:

Installation

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 r-txrevise

and update with::

   mamba update r-txrevise

To create a new environment, run:

mamba create --name myenvname r-txrevise

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 quay.io/biocontainers/r-txrevise:<tag>

(see `r-txrevise/tags`_ for valid values for ``<tag>``)

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Link to this page

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