- recipe bioconductor-rsvsim
RSVSim: an R/Bioconductor package for the simulation of structural variations
RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.
- package bioconductor-rsvsim¶
- depends bioconductor-biostrings:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-shortread:
- depends r-base:
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-rsvsim and update with:: mamba update bioconductor-rsvsim
To create a new environment, run:
mamba create --name myenvname bioconductor-rsvsim
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-rsvsim:<tag> (see `bioconductor-rsvsim/tags`_ for valid values for ``<tag>``)