recipe bioconductor-diffhic

Differential Analyis of Hi-C Data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/diffHic.html

License:

GPL-3

Recipe:

/bioconductor-diffhic/meta.yaml

Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.

package bioconductor-diffhic

(downloads) docker_bioconductor-diffhic

versions:
1.34.0-01.32.0-01.30.0-11.30.0-01.26.0-21.26.0-11.26.0-01.24.0-01.22.0-1

1.34.0-01.32.0-01.30.0-11.30.0-01.26.0-21.26.0-11.26.0-01.24.0-01.22.0-11.22.0-01.20.0-01.18.0-01.16.0-11.14.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-bsgenome:

>=1.70.1,<1.71.0a0

depends bioconductor-csaw:

>=1.36.0,<1.37.0

depends bioconductor-csaw:

>=1.36.0,<1.37.0a0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-edger:

>=4.0.2,<4.1.0a0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomeinfodb:

>=1.38.1,<1.39.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-interactionset:

>=1.30.0,<1.31.0

depends bioconductor-interactionset:

>=1.30.0,<1.31.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-limma:

>=3.58.1,<3.59.0a0

depends bioconductor-rhdf5:

>=2.46.0,<2.47.0

depends bioconductor-rhdf5:

>=2.46.1,<2.47.0a0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0a0

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-locfit:

depends r-rcpp:

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-diffhic

and update with::

   mamba update bioconductor-diffhic

To create a new environment, run:

mamba create --name myenvname bioconductor-diffhic

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-diffhic:<tag>

(see `bioconductor-diffhic/tags`_ for valid values for ``<tag>``)

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