Package: HiCcompare 1.29.0

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_1.29.0.tar.gz
HiCcompare_1.29.0.zip(r-4.5)HiCcompare_1.29.0.zip(r-4.4)HiCcompare_1.29.0.zip(r-4.3)
HiCcompare_1.29.0.tgz(r-4.4-any)HiCcompare_1.29.0.tgz(r-4.3-any)
HiCcompare_1.29.0.tar.gz(r-4.5-noble)HiCcompare_1.29.0.tar.gz(r-4.4-noble)
HiCcompare_1.29.0.tgz(r-4.4-emscripten)HiCcompare_1.29.0.tgz(r-4.3-emscripten)
HiCcompare.pdf |HiCcompare.html✨
HiCcompare/json (API)
NEWS

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

Peer review:

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

Datasets:
  • 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
  • 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
  • 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.IS - Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution
  • nhek.IS - Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution

On BioConductor:HiCcompare-1.29.0(bioc 3.21)HiCcompare-1.28.0(bioc 3.20)

softwarehicsequencingnormalizationdifference-detectionhi-cvisualization

8.56 score 19 stars 5 packages 45 scripts 459 downloads 4 mentions 24 exports 75 dependencies

Last updated 2 months agofrom:07988eb87b. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:cooler2bedpecooler2sparsecreate.hic.tablefilter_paramsfull2sparsehic_comparehic_diffhic_loesshic_simulatehicpro2bedpeKRnormMA_normmake_InteractionSetmanhattan_plotMD.plot1MD.plot2remove_centromereSCNsim_matrixsim.other.methodssparse2fullsplit_centromeretotal_sumvisualize_pvals

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablegtoolshttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigR6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

HiCcompare Vignette

John Stansfield, Mikhail Dozmorov

Rendered fromHiCcompare-vignette.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
HiCcompareHiCcompare-package HiCcompare
Hi-C data from two regions of the brain at 100KB resolutionbrain_table
Locations of the centromeres for hg19centromere_locations
Hi-C data in the cooler formatcooler
Read a .cool file into R and output the data in BEDPE formatcooler2bedpe
Transform a .cool file to a sparse upper triangular matrix for input into hic_loesscooler2sparse
Create hic.table object from a sparse upper triangular Hi-C matrixcreate.hic.table
Determine the A quantile cutoff to be usedfilter_params
Transfrom a full Hi-C contact matrix to a sparse upper triangular matrixfull2sparse
BED file for hg19 blacklisted regionshg19_blacklist
BED file for hg38 blacklisted regionshg38_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() insteadhic_diff
Perform joint loess normalization on two Hi-C datasetshic_loess
Simulate a Hi-C matrix and perform HiCcompare analysis on ithic_simulate
Convert HiC-Pro results to BEDPE formathicpro2bedpe
Hi-C data from HMEC cell line - chromosome 10 at 500kb resolutionHMEC.chr10
Hi-C data from HMEC cell line - chromosome 22 at 500kb resolutionHMEC.chr22
Hi-C data from HMEC cell line - chromosome 22 at 500kb resolutionhmec.IS
Performs KR (Knight-Ruiz) normalization on a Hi-C matrixKRnorm
Perform MA normalization on a hic.table objectMA_norm
Convert HiCdiff results to InteractionSet objectmake_InteractionSet
Create a Manhattan plot for the results of HiCcomparemanhattan_plot
Visualize the MD plot before and after loess normalizationMD.plot1
Visualize the MD plot.MD.plot2
Hi-C data from NHEK cell line - chromosome 10 at 500kb resolutionNHEK.chr10
Hi-C data from NHEK cell line - chromosome 22 at 500kb resolutionNHEK.chr22
Hi-C data from NHEK cell line - chromosome 22 at 500kb resolutionnhek.IS
Function to remove centromere columns and rows from a full Hi-C contact matrixremove_centromere
SCN normalization from Cournac 2012SCN
Simulate 2 Hi-C matrices with differencessim_matrix
Compare other normalization methods on simulated datasim.other.methods
Transform a sparse upper triangular matrix to a full Hi-C contact matrixsparse2full
Function to split hic.table into 2 subsets at the centromeresplit_centromere
Total sum normalization for a list of hic.table objectstotal_sum
Function to visualize p-values from HiCcompare resultsvisualize_pvals