- recipe bioconductor-hicdoc
A/B compartment detection and differential analysis
- Homepage:
https://bioconductor.org/packages/3.16/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:
1.0.0-0
- Depends:
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-biocparallel
>=1.32.0,<1.33.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-interactionset
>=1.26.0,<1.27.0
bioconductor-multihiccompare
>=1.16.0,<1.17.0
bioconductor-rhdf5
>=2.42.0,<2.43.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-summarizedexperiment
>=1.28.0,<1.29.0
bioconductor-zlibbioc
>=1.44.0,<1.45.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
libstdcxx-ng
>=12
r-base
>=4.2,<4.3.0a0
r-rcpp
>=0.12.8
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-hicdoc
and update with:
conda update bioconductor-hicdoc
or 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)