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

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Documentation for package ‘multiHiCcompare’ version 1.26.0

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cyclic_loess Cyclic Loess normalization for Hi-C data
exportJuicebox Export multiHiCcompare results for visualization in Juicebox
fastlo Perform fast loess normalization on a Hi-C experiment
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.
Hicexp-class An S4 class for working with Hi-C data
hicexp2 hicexp object with 4 samples from two groups.
hicexp_diff hicexp object with 7 samples from two groups.
hic_exactTest Perform exact test based difference detection on a Hi-C experiment
hic_filter Perform filtering on a Hi-C experiment
hic_glm Function to perform GLM differential analysis on Hi-C experiment
hic_scale Perform library scaling on a hicexp object
hic_table Print the hic_table
hic_table-method Print the hic_table
make_hicexp Make Hi-C experiment object from data
manhattan_hicexp Manhattan plot function for results of multiHiCcompare
MD_composite Plot a composite MD plot with the results of a comparison
MD_hicexp Make MD plots for all combinations of a condition
meta Print the metadata
meta-method Print the metadata
normalized Print the indicator for if the data is normalized
normalized-method Print the indicator for if the data is normalized
perm_test Perform a permutation test to check enrichment of a genomic feature with DIRs detected by multiHiCcompare
plot_counts Plot the count results from topDirs
plot_pvals Plot the p-value results from topDirs
pval_heatmap Function to visualize p-values from multiHiCcompare results
resolution Print the resolution
resolution-method Print the resolution
results Print the results
results-method Print the results
show-method Print information about a HiCexp object
smartApply Function to apply either biocParallel or standard lapply
topDirs Filter results of multiHiCcompare