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

Versions:

1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-1, 

1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-1,  1.0.0-0

Depends:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomeinfodbdata >=1.2.0,<1.3.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-hiccompare >=1.20.0,<1.21.0

• r-aggregation

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-dplyr

• r-pbapply

• r-pheatmap

• r-qqman

Required By:

• bioconductor-hicdoc

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>)

Download stats

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