recipe bioconductor-multihiccompare

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/multiHiCcompare.html

License

MIT + file LICENSE

Recipe

/bioconductor-multihiccompare/meta.yaml

package bioconductor-multihiccompare

(downloads) docker_bioconductor-multihiccompare

Versions

1.2.0-1, 1.0.0-1, 1.0.0-0

Depends
Required By

Installation

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

conda install bioconductor-multihiccompare

and update with:

conda update bioconductor-multihiccompare

or use the docker container:

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

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