recipe bioconductor-hiccompare

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Homepage

https://bioconductor.org/packages/3.10/bioc/html/HiCcompare.html

License

MIT + file LICENSE

Recipe

/bioconductor-hiccompare/meta.yaml

Links

biotools: HiCcompare, doi: 10.1186/s12859-018-2288-x

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

package bioconductor-hiccompare

(downloads) docker_bioconductor-hiccompare

Versions

1.8.0-0, 1.6.0-1, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-hiccompare

and update with:

conda update bioconductor-hiccompare

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-hiccompare:<tag>

(see bioconductor-hiccompare/tags for valid values for <tag>)