Package: HiCDOC

Title: A/B compartment detection and differential analysis

Version: 1.11.1

Date: 2022-11-30

Authors@R: c(

person("Kurylo", "Cyril", email = "[email protected]", role = c("aut")),

person("Zytnicki", "Matthias", email = "[email protected]", role = c("aut")),

person("Foissac", "Sylvain", email = "[email protected]", role = c("aut")),

person("Maigné", "Élise", email = "[email protected]", role = c("aut", "cre")))

Description:

HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning

to predict A/B compartments from multiple replicates, and detects

significant compartment changes between experiment conditions.

It provides a collection of functions assembled into a pipeline to filter

and normalize the data, predict the compartments and visualize the results.

It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or

`.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.

License: LGPL-3

Encoding: UTF-8

SystemRequirements: C++11

Depends:

InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0)

Imports:

methods,

ggplot2,

Rcpp (>= 0.12.8),

stats,

S4Vectors,

gtools,

pbapply,

BiocParallel,

BiocGenerics,

grid,

cowplot,

gridExtra,

data.table,

multiHiCcompare,

GenomeInfoDb

LinkingTo: Rcpp

Suggests:

knitr,

rmarkdown,

testthat,

BiocStyle,

BiocManager,

rhdf5

RoxygenNote: 7.3.2

biocViews:

HiC, DNA3DStructure, Normalization, Sequencing, Software, Clustering

VignetteBuilder: knitr

URL: https://github.com/mzytnicki/HiCDOC

BugReports: https://github.com/mzytnicki/HiCDOC/issues