Package: scHiCcompare 1.5.0

My Nguyen

scHiCcompare: Differential Analysis of Single-cell Hi-C Data

This package provides functions for differential chromatin interaction analysis between two single-cell Hi-C data groups. It includes tools for imputation, normalization, and differential analysis of chromatin interactions. The package implements pooling techniques for imputation and offers methods to normalize and test for differential interactions across single-cell Hi-C datasets.

Authors:My Nguyen [aut, cre], Mikhail Dozmorov [aut]

scHiCcompare_1.5.0.tar.gz
scHiCcompare_1.5.0.zip(r-4.7)scHiCcompare_1.5.0.zip(r-4.6)scHiCcompare_1.5.0.zip(r-4.5)
scHiCcompare_1.5.0.tgz(r-4.6-any)scHiCcompare_1.5.0.tgz(r-4.5-any)
scHiCcompare_1.5.0.tar.gz(r-4.7-any)scHiCcompare_1.5.0.tar.gz(r-4.6-any)
scHiCcompare_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scHiCcompare/json (API)
NEWS

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

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

Datasets:
  • ODC.bandnorm_chr20_1 - ScHi-C data from oligodendrocyte (ODC) cell type - chromosome 20 at 1 MB resolution
  • scHiC.table_MG_chr22 - ScHi-C table from microglia (MG) cell type - chromosome 22 at 1 MB resolution
  • scHiC.table_ODC_chr22 - ScHi-C table from oligodendrocyte (ODC) cell type - chromosome 22 at 1 MB resolution

On BioConductor:scHiCcompare-1.5.0(bioc 3.24)scHiCcompare-1.4.0(bioc 3.23)

softwaresinglecellhicsequencingnormalizationchromatinschi-csingle-cell

4.48 score 6 scripts 243 downloads 9 exports 133 dependencies

Last updated from:b574f248db. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE208
linux-devel-x86_64WARNING384
source / vignettesOK300
linux-release-x86_64WARNING403
macos-release-arm64WARNING190
macos-oldrel-arm64WARNING169
windows-develWARNING322
windows-releaseWARNING270
windows-oldrelWARNING242
wasm-releaseOK180

Exports:plot_HiCmatrix_heatmapplot_imputed_distance_diagnosticprint.scHiCcomparepseudo_bulkHicread_filesscHiC_bulk_comparescHiC_tablescHiCcomparescHiCcompare_impute

Dependencies:abindbackportsBHBiobaseBiocGenericsbiocmakeBiocParallelbitbit64bootbroomcarcarDataclicliprcodetoolscolorspacecorrplotcowplotcpp11crayondata.tableDBIDelayedArrayDerivdir.expirydoBydplyrfarverfilelockforcatsforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesggplot2glmnetgluegridExtragtablegtoolshavenHiCcomparehmsInteractionSetIRangesisobanditeratorsjomoKernSmoothlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmgcvmicemiceaddsmicrobenchmarkminqamitmlmitoolsmodelrnlmenloptrnnetnumDerivordinalpanpbkrtestpheatmappillarpkgconfigprettyunitsprogresspurrrquantregR6rangerrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrhdf5rhdf5filtersRhdf5librlangrpartrstatixS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDatetzdbucminfurcautf8vctrsviridisLitevroomwithrXVectorzoo

scHiCcompare Vignette

My Nguyen, Mikhail Dozmorov

Rendered fromScHiCcompare.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-04-01
Started: 2024-10-07