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HCT116_r1
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A 4 column sparse matrix for a Hi-C matrix. |
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HCT116_r2
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A 4 column sparse matrix for a Hi-C matrix. |
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HCT116_r3
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A 4 column sparse matrix for a Hi-C matrix. |
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HCT116_r4
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A 4 column sparse matrix for a Hi-C matrix. |
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HCT116_r5
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A 4 column sparse matrix for a Hi-C matrix. |
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HCT116_r6
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A 4 column sparse matrix for a Hi-C matrix. |
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Hicexp-class
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An S4 class for working with Hi-C data |
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MD_composite()
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Plot a composite MD plot with the results of a comparison |
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MD_hicexp()
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Make MD plots for all combinations of a condition |
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cyclic_loess()
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Cyclic Loess normalization for Hi-C data |
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exportJuicebox()
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Export multiHiCcompare results for visualization in Juicebox |
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fastlo()
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Perform fast loess normalization on a Hi-C experiment |
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hg19_cyto
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A GenomicRanges object containing centromeric, gvar, and stalk regions. |
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hg38_cyto
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A GenomicRanges object containing centromeric, gvar, and stalk regions. |
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hic_exactTest()
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Perform exact test based difference detection on a Hi-C experiment |
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hic_filter()
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Perform filtering on a Hi-C experiment |
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hic_glm()
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Function to perform GLM differential analysis on Hi-C experiment |
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hic_scale()
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Perform library scaling on a hicexp object |
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hic_table()
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Print the hic_table |
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hicexp2
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hicexp object with 4 samples from two groups. |
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hicexp_diff
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hicexp object with 7 samples from two groups. |
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make_hicexp()
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Make Hi-C experiment object from data |
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manhattan_hicexp()
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Manhattan plot function for results of multiHiCcompare |
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meta()
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Print the metadata |
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normalized()
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Print the indicator for if the data is normalized |
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perm_test()
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Perform a permutation test to check enrichment of a genomic
feature with DIRs detected by multiHiCcompare |
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plot_counts()
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Plot the count results from topDirs |
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plot_pvals()
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Plot the p-value results from topDirs |
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pval_heatmap()
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Function to visualize p-values from multiHiCcompare results |
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resolution()
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Print the resolution |
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results()
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Print the results |
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show(<Hicexp>)
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Print information about a HiCexp object |
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smartApply()
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Function to apply either biocParallel or standard lapply |
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topDirs()
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Filter results of multiHiCcompare |