Man pages for dozmorovlab/HiCdiff
HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets

coolerHi-C data in the cooler format
cooler2sparseTransform a .cool file to a sparse upper triangular matrix...
create.hic.tableCreate hic.table object from a sparse upper triangular Hi-C...
full2sparseTransfrom a full Hi-C contact matrix to a sparse upper...
hic_diffDetect differences between two jointly normalized Hi-C...
HiCdiff-packageHiCdiff
hic_loessPerform joint loess normalization on two Hi-C datasets
hic_simulateSimulate a Hi-C matrix and perform hic_diff analysis on it
HMEC.chr10Hi-C data from HMEC cell line - chromosome 10 at 500kb...
HMEC.chr22Hi-C data from HMEC cell line - chromosome 22 at 500kb...
hmec.ISHi-C data from HMEC cell line - chromosome 22 at 500kb...
KRnormPerforms KR (Knight-Ruiz) normalization on a Hi-C matrix
make_InteractionSetConvert HiCdiff results to InteractionSet object
MA_normPerform MA normalization on a hic.table object
MD.plot1Visualize the MD plot before and after loess normalization
MD.plot2Visualize the MD plot.
NHEK.chr10Hi-C data from NHEK cell line - chromosome 10 at 500kb...
NHEK.chr22Hi-C data from NHEK cell line - chromosome 22 at 500kb...
nhek.ISHi-C data from NHEK cell line - chromosome 22 at 500kb...
remove_centromereFunction to remove centromere columns and rows from a full...
SCNSCN normalization from Cournac 2012
sim.other.methodsCompare other normalization methods on simulated data
sparse2fullTransform a sparse upper triangular matrix to a full Hi-C...
dozmorovlab/HiCdiff documentation built on July 13, 2017, 10:13 a.m.