- 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:
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-base
>=4.2,<4.3.0a0
- 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-multihiccompare/README.html)