- recipe bioconductor-rgntx
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.
- package bioconductor-rgntx¶
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicfeatures:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-regioner:
- depends bioconductor-s4vectors:
- depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:
- depends r-base:
- depends r-ggplot2:
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-rgntx and update with:: mamba update bioconductor-rgntx
To create a new environment, run:
mamba create --name myenvname bioconductor-rgntx
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/bioconductor-rgntx:<tag> (see `bioconductor-rgntx/tags`_ for valid values for ``<tag>``)