Package: HiCcompare 1.35.0

Mikhail Dozmorov

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

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.

Authors:Mikhail Dozmorov [aut, cre], Kellen Cresswell [aut], John Stansfield [aut]

HiCcompare_1.35.0.tar.gz
HiCcompare_1.35.0.zip(r-4.7)HiCcompare_1.35.0.zip(r-4.6)HiCcompare_1.35.0.zip(r-4.5)
HiCcompare_1.35.0.tgz(r-4.6-any)HiCcompare_1.35.0.tgz(r-4.5-any)
HiCcompare_1.35.0.tar.gz(r-4.7-any)HiCcompare_1.35.0.tar.gz(r-4.6-any)
HiCcompare_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HiCcompare/json (API)

# Install 'HiCcompare' in R:

install.packages('HiCcompare', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dozmorovlab/hiccompare/issues

Datasets:

brain_table - Hi-C data from two regions of the brain at 100KB resolution
centromere_locations - Locations of the centromeres for hg19
cooler - Hi-C data in the cooler format
hg19_blacklist - BED file for hg19 blacklisted regions
hg38_blacklist - BED file for hg38 blacklisted regions
HMEC.chr10 - Hi-C data from HMEC cell line - chromosome 10 at 500kb resolution
HMEC.chr22 - Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution
hmec.IS - Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution
NHEK.chr10 - Hi-C data from NHEK cell line - chromosome 10 at 500kb resolution
NHEK.chr22 - Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution
nhek.IS - Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution

On BioConductor:HiCcompare-1.35.0(bioc 3.24)HiCcompare-1.34.0(bioc 3.23)

software hic sequencing normalization difference-detection hi-c visualization

8.85 score 23 stars 5 packages 74 scripts 4 mentions 24 exports 64 dependencies

Last updated from:52adf7edf3. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	230
linux-devel-x86_64	NOTE	392
source / vignettes	OK	275
linux-release-x86_64	NOTE	372
macos-release-arm64	NOTE	170
macos-oldrel-arm64	NOTE	160
windows-devel	NOTE	269
windows-release	NOTE	305
windows-oldrel	NOTE	284
wasm-release	OK	190

Exports:cooler2bedpe cooler2sparse create.hic.table filter_params full2sparse hic_compare hic_diff hic_loess hic_simulate hicpro2bedpe KRnorm MA_norm make_InteractionSet manhattan_plot MD.plot1 MD.plot2 remove_centromere SCN sim_matrix sim.other.methods sparse2full split_centromere total_sum visualize_pvals

Dependencies:abind BH Biobase BiocGenerics biocmake BiocParallel cli codetools cpp11 data.table DelayedArray dir.expiry dplyr farver filelock formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gridExtra gtable gtools InteractionSet IRanges isoband KernSmooth labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mgcv nlme pheatmap pillar pkgconfig R6 RColorBrewer Rcpp rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SummarizedExperiment tibble tidyselect utf8 vctrs viridisLite withr XVector

HiCcompare Vignette

Rendered fromHiCcompare-vignette.Rmdusingknitr::rmarkdown

Last update: 2023-06-04
Started: 2017-07-11

Help page	Topics
HiCcompare	HiCcompare-package HiCcompare
Hi-C data from two regions of the brain at 100KB resolution	brain_table
Locations of the centromeres for hg19	centromere_locations
Hi-C data in the cooler format	cooler
Read a .cool file into R and output the data in BEDPE format	cooler2bedpe
Transform a .cool file to a sparse upper triangular matrix for input into hic_loess	cooler2sparse
Create hic.table object from a sparse upper triangular Hi-C matrix	create.hic.table
Determine the A quantile cutoff to be used	filter_params
Transfrom a full Hi-C contact matrix to a sparse upper triangular matrix	full2sparse
BED file for hg19 blacklisted regions	hg19_blacklist
BED file for hg38 blacklisted regions	hg38_blacklist
Detect differences between two jointly normalized Hi-C datasets.	hic_compare
Detect differences between two jointly normalized Hi-C datasets. OLD METHOD; USE hic_compare() instead	hic_diff
Perform joint loess normalization on two Hi-C datasets	hic_loess
Simulate a Hi-C matrix and perform HiCcompare analysis on it	hic_simulate
Convert HiC-Pro results to BEDPE format	hicpro2bedpe
Hi-C data from HMEC cell line - chromosome 10 at 500kb resolution	HMEC.chr10
Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution	HMEC.chr22
Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution	hmec.IS
Performs KR (Knight-Ruiz) normalization on a Hi-C matrix	KRnorm
Perform MA normalization on a hic.table object	MA_norm
Convert HiCdiff results to InteractionSet object	make_InteractionSet
Create a Manhattan plot for the results of HiCcompare	manhattan_plot
Visualize the MD plot before and after loess normalization	MD.plot1
Visualize the MD plot.	MD.plot2
Hi-C data from NHEK cell line - chromosome 10 at 500kb resolution	NHEK.chr10
Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution	NHEK.chr22
Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution	nhek.IS
Function to remove centromere columns and rows from a full Hi-C contact matrix	remove_centromere
SCN normalization from Cournac 2012	SCN
Simulate 2 Hi-C matrices with differences	sim_matrix
Compare other normalization methods on simulated data	sim.other.methods
Transform a sparse upper triangular matrix to a full Hi-C contact matrix	sparse2full
Function to split hic.table into 2 subsets at the centromere	split_centromere
Total sum normalization for a list of hic.table objects	total_sum
Function to visualize p-values from HiCcompare results	visualize_pvals

Package: HiCcompare 1.35.0

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

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