- recipe bioconductor-fcscan
fcScan for detecting clusters of coordinates with user defined options
This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.
- package bioconductor-fcscan¶
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-rtracklayer:
- depends bioconductor-summarizedexperiment:
- depends bioconductor-variantannotation:
- depends r-base:
- depends r-doparallel:
- depends r-foreach:
- depends r-plyr:
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-fcscan and update with:: mamba update bioconductor-fcscan
To create a new environment, run:
mamba create --name myenvname bioconductor-fcscan
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-fcscan:<tag> (see `bioconductor-fcscan/tags`_ for valid values for ``<tag>``)