Introduction | Installation | scHiCcompare function | Overview | Input | Prepare input folders | Example of real analysis | Output | Output objects from the R function | Externally saved output files | Example of output | Helper functions | Heatmap HiC matrix plot | Imputation Diagnostic plot | Others | Download scHiC data | Import scHiC data in R | Session Info
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
scHiCcompare/json (API)
| # 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
Last updated from:b574f248db. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 210 | ||
| linux-devel-x86_64 | WARNING | 338 | ||
| source / vignettes | OK | 303 | ||
| linux-release-x86_64 | WARNING | 397 | ||
| macos-release-arm64 | WARNING | 232 | ||
| macos-oldrel-arm64 | WARNING | 271 | ||
| windows-devel | WARNING | 270 | ||
| windows-release | WARNING | 274 | ||
| windows-oldrel | WARNING | 291 | ||
| wasm-release | OK | 200 |
Exports:plot_HiCmatrix_heatmapplot_imputed_distance_diagnosticprint.scHiCcomparepseudo_bulkHicread_filesscHiC_bulk_comparescHiC_tablescHiCcomparescHiCcompare_impute
Dependencies:abindbackportsBHBiobaseBiocGenericsbiocmakeBiocParallelbitbit64bootbroomcarcarDataclicliprcodetoolscolorspacecorrplotcowplotcpp11crayondata.tableDBIDelayedArrayDerivdir.expirydoBydplyrfarverfilelockforcatsforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesggplot2glmnetgluegridExtragtablegtoolshavenHiCcomparehmsInteractionSetIRangesisobanditeratorsjomoKernSmoothlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmgcvmicemiceaddsminqamitmlmitoolsmodelrnlmenloptrnnetnumDerivordinalpanpbkrtestpheatmappillarpkgconfigprettyunitsprogresspurrrquantregR6rangerrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrhdf5rhdf5filtersRhdf5librlangrpartrstatixS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDatetzdbucminfurcautf8vctrsviridisLitevroomwithrXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| scHi-C data from oligodendrocyte (ODC) cell type - chromosome 20 at 1 MB resolution | ODC.bandnorm_chr20_1 |
| Plot Hi-C Interaction Matrix Heatmap | plot_HiCmatrix_heatmap |
| Plot Imputed Distance Diagnostic | plot_imputed_distance_diagnostic |
| Print method for `scHiCcompare` objects | print.scHiCcompare |
| Generate Pseudo-bulk Hi-C Data | pseudo_bulkHic |
| Read Files for scHi-C Dataset | read_files |
| Compare Bulk Hi-C Data | scHiC_bulk_compare |
| Create scHiC Interaction Frequency Table | scHiC_table |
| scHi-C table from microglia (MG) cell type - chromosome 22 at 1 MB resolution | scHiC.table_MG_chr22 |
| scHi-C table from oligodendrocyte (ODC) cell type - chromosome 22 at 1 MB resolution | scHiC.table_ODC_chr22 |
| ScHiCcompare: Differential Analysis of Single-Cell Hi-C Data | scHiCcompare |
| Random Forest Imputation with Pooling options for scHi-C Data | scHiCcompare_impute |
