recipe bioconductor-hicdoc

A/B compartment detection and differential analysis

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/HiCDOC.html

License:

LGPL (>= 3)

Recipe:

/bioconductor-hicdoc/meta.yaml

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:

1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-interactionset:

>=1.28.0,<1.29.0

depends bioconductor-multihiccompare:

>=1.18.0,<1.19.0

depends bioconductor-rhdf5:

>=2.44.0,<2.45.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-zlibbioc:

>=1.46.0,<1.47.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggextra:

depends r-ggplot2:

depends r-ggpubr:

depends r-gridextra:

depends r-gtools:

depends r-pbapply:

depends r-rcpp:

>=0.12.8

requirements:

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 myenvname being 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>``)

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