- recipe bioconductor-tin
Transcriptome instability analysis
The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.
- package bioconductor-tin¶
- depends bioconductor-impute:
- depends r-aroma.affymetrix:
- depends r-base:
- depends r-data.table:
- depends r-squash:
- depends r-stringr:
- depends r-wgcna:
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-tin and update with:: mamba update bioconductor-tin
To create a new environment, run:
mamba create --name myenvname bioconductor-tin
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-tin:<tag> (see `bioconductor-tin/tags`_ for valid values for ``<tag>``)