recipe bioconductor-multihiccompare

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/multiHiCcompare.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-multihiccompare/meta.yaml

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.

package bioconductor-multihiccompare

(downloads) docker_bioconductor-multihiccompare

Versions:
1.16.0-01.12.0-01.10.0-01.8.0-11.8.0-01.6.0-01.4.0-01.2.0-11.0.0-1

1.16.0-01.12.0-01.10.0-01.8.0-11.8.0-01.6.0-01.4.0-01.2.0-11.0.0-11.0.0-0

Depends:
Required By:

Installation

With an activated Bioconda channel (see 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>)

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