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. |
Hicexp-class
|
An S4 class for working with Hi-C data |
MD_composite()
|
Plot a composite MD plot with the results of a comparison |
MD_hicexp()
|
Make MD plots for all combinations of a condition |
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 |
hg19_cyto
|
A GenomicRanges object containing centromeric, gvar, and stalk regions. |
hg38_cyto
|
A GenomicRanges object containing centromeric, gvar, and stalk regions. |
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 |
hicexp2
|
hicexp object with 4 samples from two groups. |
hicexp_diff
|
hicexp object with 7 samples from two groups. |
make_hicexp()
|
Make Hi-C experiment object from data |
manhattan_hicexp()
|
Manhattan plot function for results of multiHiCcompare |
meta()
|
Print the metadata |
normalized()
|
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 |
results()
|
Print the results |
show(<Hicexp>)
|
Print information about a HiCexp object |
smartApply()
|
Function to apply either biocParallel or standard lapply |
topDirs()
|
Filter results of multiHiCcompare |