- recipe bioconductor-scanmir
A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
- package bioconductor-scanmir¶
- depends bioconductor-biocparallel:
- depends bioconductor-biostrings:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-cowplot:
- depends r-data.table:
- depends r-ggplot2:
- depends r-ggseqlogo:
- depends r-stringi:
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-scanmir and update with:: mamba update bioconductor-scanmir
To create a new environment, run:
mamba create --name myenvname bioconductor-scanmir
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-scanmir:<tag> (see `bioconductor-scanmir/tags`_ for valid values for ``<tag>``)