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HMEC.chr10
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Hi-C data from HMEC cell line - chromosome 10 at 500kb resolution |
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HMEC.chr22
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Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution |
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HiCcompare-package
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HiCcompare |
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KRnorm()
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Performs KR (Knight-Ruiz) normalization on a Hi-C matrix |
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MA_norm()
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Perform MA normalization on a hic.table object |
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MD.plot1()
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Visualize the MD plot before and after loess normalization |
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MD.plot2()
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Visualize the MD plot. |
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NHEK.chr10
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Hi-C data from NHEK cell line - chromosome 10 at 500kb resolution |
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NHEK.chr22
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Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution |
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SCN()
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SCN normalization from Cournac 2012 |
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brain_table
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Hi-C data from two regions of the brain at 100KB resolution |
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centromere_locations
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Locations of the centromeres for hg19 |
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cooler
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Hi-C data in the cooler format |
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cooler2bedpe()
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Read a .cool file into R and output the data in BEDPE format |
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cooler2sparse()
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Transform a .cool file to a sparse upper triangular matrix for input into
hic_loess |
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create.hic.table()
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Create hic.table object from a sparse upper triangular Hi-C matrix |
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filter_params()
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Determine the A quantile cutoff to be used |
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full2sparse()
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Transfrom a full Hi-C contact matrix to a sparse upper triangular matrix |
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get_CNV()
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Function to get the locations of copy number variations |
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hg19_blacklist
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BED file for hg19 blacklisted regions |
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hg38_blacklist
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BED file for hg38 blacklisted regions |
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hic_compare()
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Detect differences between two jointly normalized Hi-C datasets. |
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hic_diff()
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Detect differences between two jointly normalized Hi-C datasets. OLD METHOD; USE hic_compare() instead |
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hic_loess()
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Perform joint loess normalization on two Hi-C datasets |
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hic_simulate()
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Simulate a Hi-C matrix and perform HiCcompare analysis on it |
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hicpro2bedpe()
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Convert HiC-Pro results to BEDPE format |
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hmec.IS
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Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution |
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make_InteractionSet()
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Convert HiCdiff results to InteractionSet object |
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manhattan_plot()
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Create a Manhattan plot for the results of HiCcompare |
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nhek.IS
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Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution |
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remove_centromere()
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Function to remove centromere columns and rows from a full Hi-C
contact matrix |
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sim.other.methods()
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Compare other normalization methods on simulated data |
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sim_matrix()
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Simulate 2 Hi-C matrices with differences |
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sparse2full()
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Transform a sparse upper triangular matrix to a full Hi-C contact matrix |
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split_centromere()
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Function to split hic.table into 2 subsets at the centromere |
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total_sum()
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Total sum normalization for a list of hic.table objects |
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visualize_pvals()
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Function to visualize p-values from HiCcompare results |