- recipe bioconductor-hicdoc
A/B compartment detection and differential analysis
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/HiCDOC.html
- License:
LGPL-3
- Recipe:
HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.
- package bioconductor-hicdoc¶
- versions:
1.8.0-0,1.4.0-0,1.2.0-0,1.0.0-1,1.0.0-0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0a0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0a0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0a0- depends bioconductor-interactionset:
>=1.34.0,<1.35.0- depends bioconductor-interactionset:
>=1.34.0,<1.35.0a0- depends bioconductor-multihiccompare:
>=1.24.0,<1.25.0- depends bioconductor-multihiccompare:
>=1.24.0,<1.25.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0a0- depends bioconductor-zlibbioc:
>=1.52.0,<1.53.0- depends bioconductor-zlibbioc:
>=1.52.0,<1.53.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=13- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx:
>=13- depends libzlib:
>=1.3.1,<2.0a0- depends r-base:
>=4.4,<4.5.0a0- depends r-cowplot:
- depends r-data.table:
- depends r-ggplot2:
- depends r-gridextra:
- depends r-gtools:
- depends r-pbapply:
- depends r-rcpp:
>=0.12.8- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
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-hicdoc and update with:: mamba update bioconductor-hicdoc
To create a new environment, run:
mamba create --name myenvname bioconductor-hicdoc
with
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-hicdoc:<tag> (see `bioconductor-hicdoc/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-hicdoc/README.html)
