- recipe bioconductor-diffhic
Differential Analysis of Hi-C Data
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/diffHic.html
- License:
GPL-3
- Recipe:
- Links:
biotools: diffhic
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¶
- versions:
1.38.0-0,1.34.0-1,1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.26.0-2,1.26.0-1,1.26.0-0,1.38.0-0,1.34.0-1,1.34.0-0,1.32.0-0,1.30.0-1,1.30.0-0,1.26.0-2,1.26.0-1,1.26.0-0,1.24.0-0,1.22.0-1,1.22.0-0,1.20.0-0,1.18.0-0,1.16.0-1,1.14.0-0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0a0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0a0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0a0- depends bioconductor-csaw:
>=1.40.0,<1.41.0- depends bioconductor-csaw:
>=1.40.0,<1.41.0a0- depends bioconductor-edger:
>=4.4.0,<4.5.0- depends bioconductor-edger:
>=4.4.0,<4.5.0a0- 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-iranges:
>=2.40.0,<2.41.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0a0- depends bioconductor-limma:
>=3.62.0,<3.63.0- depends bioconductor-limma:
>=3.62.0,<3.63.0a0- depends bioconductor-rhdf5:
>=2.50.0,<2.51.0- depends bioconductor-rhdf5:
>=2.50.0,<2.51.0a0- depends bioconductor-rhtslib:
>=3.2.0,<3.3.0- depends bioconductor-rhtslib:
>=3.2.0,<3.3.0a0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0- depends bioconductor-rsamtools:
>=2.22.0,<2.23.0a0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0a0- 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 liblzma:
>=5.6.3,<6.0a0- depends libstdcxx:
>=13- depends libzlib:
>=1.3.1,<2.0a0- depends r-base:
>=4.4,<4.5.0a0- depends r-locfit:
- depends r-rcpp:
- requirements:
- additional platforms:
linux-aarch64
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
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-diffhic:<tag> (see `bioconductor-diffhic/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-diffhic/README.html)
