Package: multiHiCcompare 1.25.0

Mikhail Dozmorov

multiHiCcompare: Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

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.

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

multiHiCcompare_1.25.0.tar.gz
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multiHiCcompare.pdf |multiHiCcompare.html✨
multiHiCcompare/json (API)
NEWS

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

Peer review:

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

Datasets:
  • HCT116_r1 - A 4 column sparse matrix for a Hi-C matrix.
  • HCT116_r2 - A 4 column sparse matrix for a Hi-C matrix.
  • HCT116_r3 - A 4 column sparse matrix for a Hi-C matrix.
  • HCT116_r4 - A 4 column sparse matrix for a Hi-C matrix.
  • HCT116_r5 - A 4 column sparse matrix for a Hi-C matrix.
  • HCT116_r6 - A 4 column sparse matrix for a Hi-C matrix.
  • hg19_cyto - A GenomicRanges object containing centromeric, gvar, and stalk regions.
  • hg38_cyto - A GenomicRanges object containing centromeric, gvar, and stalk regions.
  • hicexp2 - Hicexp object with 4 samples from two groups.
  • hicexp_diff - Hicexp object with 7 samples from two groups.

On BioConductor:multiHiCcompare-1.23.0(bioc 3.20)multiHiCcompare-1.22.0(bioc 3.19)

softwarehicsequencingnormalization

7.26 score 8 stars 2 packages 38 scripts 320 downloads 1 mentions 22 exports 84 dependencies

Last updated 20 days agofrom:62d7e43dd8. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:cyclic_loessexportJuiceboxfastlohic_exactTesthic_filterhic_glmhic_scalehic_tablemake_hicexpmanhattan_hicexpMD_compositeMD_hicexpmetanormalizedperm_testplot_countsplot_pvalspval_heatmapresolutionresultsshowtopDirs

Dependencies:abindaggregationaskpassBHBiobaseBiocGenericsBiocParallelcalibrateclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydplyredgeRfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpbapplypheatmappillarpkgconfigqqmanR6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalessnowSparseArraystatmodSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Visualizing multiHiCcompare results in Juicebox

John C. Stansfield & Mikhail G. Dozmorov

Rendered fromjuiceboxVisualization.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2020-11-23
Started: 2018-11-13

multiHiCcompare Vignette

John C. Stansfield & Mikhail G. Dozmorov

Rendered frommultiHiCcompare.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2020-11-23
Started: 2018-08-03

Readme and manuals

Help Manual

Help pageTopics
Cyclic Loess normalization for Hi-C datacyclic_loess
Export multiHiCcompare results for visualization in JuiceboxexportJuicebox
Perform fast loess normalization on a Hi-C experimentfastlo
A 4 column sparse matrix for a Hi-C matrix.HCT116_r1
A 4 column sparse matrix for a Hi-C matrix.HCT116_r2
A 4 column sparse matrix for a Hi-C matrix.HCT116_r3
A 4 column sparse matrix for a Hi-C matrix.HCT116_r4
A 4 column sparse matrix for a Hi-C matrix.HCT116_r5
A 4 column sparse matrix for a Hi-C matrix.HCT116_r6
A GenomicRanges object containing centromeric, gvar, and stalk regions.hg19_cyto
A GenomicRanges object containing centromeric, gvar, and stalk regions.hg38_cyto
Perform exact test based difference detection on a Hi-C experimenthic_exactTest
Perform filtering on a Hi-C experimenthic_filter
Function to perform GLM differential analysis on Hi-C experimenthic_glm
Perform library scaling on a hicexp objecthic_scale
Print the hic_tablehic_table hic_table,character,ANY-method hic_table,Hicexp-method
hicexp object with 7 samples from two groups.hicexp_diff
An S4 class for working with Hi-C dataHicexp-class
hicexp object with 4 samples from two groups.hicexp2
Make Hi-C experiment object from datamake_hicexp
Manhattan plot function for results of multiHiCcomparemanhattan_hicexp
Plot a composite MD plot with the results of a comparisonMD_composite
Make MD plots for all combinations of a conditionMD_hicexp
Print the metadatameta meta,character,ANY-method meta,Hicexp-method
Print the indicator for if the data is normalizednormalized normalized,character,ANY-method normalized,Hicexp-method
Perform a permutation test to check enrichment of a genomic feature with DIRs detected by multiHiCcompareperm_test
Plot the count results from topDirsplot_counts
Plot the p-value results from topDirsplot_pvals
Function to visualize p-values from multiHiCcompare resultspval_heatmap
Print the resolutionresolution resolution,character,ANY-method resolution,Hicexp-method
Print the resultsresults results,character,ANY-method results,Hicexp-method
Print information about a HiCexp objectshow,character,ANY-method show,Hicexp-method
Function to apply either biocParallel or standard lapplysmartApply
Filter results of multiHiCcomparetopDirs