- recipe bioconductor-hitc
High Throughput Chromosome Conformation Capture analysis
The HiTC package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.
- package bioconductor-hitc¶
- depends bioconductor-biostrings:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-rtracklayer:
- depends r-base:
- depends r-matrix:
- depends r-rcolorbrewer:
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-hitc and update with:: mamba update bioconductor-hitc
To create a new environment, run:
mamba create --name myenvname bioconductor-hitc
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-hitc:<tag> (see `bioconductor-hitc/tags`_ for valid values for ``<tag>``)