recipe bioconductor-hiccompare

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

Homepage:

https://bioconductor.org/packages/3.16/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

Versions:

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0, 

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-interactionset >=1.26.0,<1.27.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-qdnaseq >=1.34.0,<1.35.0

• bioconductor-rhdf5 >=2.42.0,<2.43.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-dplyr

• r-ggplot2

• r-gridextra

• r-gtools

• r-kernsmooth

• r-mgcv

• r-pheatmap

Required By:

• bioconductor-tadcompare

• bioconductor-spectraltad

• bioconductor-multihiccompare

Installation

With an activated Bioconda channel (see 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>)

Download stats

Link to this page

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