- recipe r-txrevise
Construct custom transcript annotations for Salmon and kallisto
Apache / Apache 2.0
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¶
- depends bioconductor-genomicfeatures:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends r-base:
- depends r-dplyr:
- depends r-ggplot2:
- depends r-purrr:
- depends r-purrrlyr:
- depends r-readr:
- depends r-tidyr:
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
myenvnamebeing 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>``)