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scHiCluster
scHiCluster
Tutorial
Tan et al. Cell 2021.
Prepare and run imputation
scRNA(MALBAC) clustering
DipC clustering at 100kb resolution
Assign DipC cells to RNA clusters
Prepare pseudobulk analyses
Generate blacklist for loop calling
Human Brain Atlas
Differentially expressed genes
DEG identification
RNA correlated loop
RNA correlated boundary
RNA correlated compartment
Differential loops
ANOVA of loop matrices across cell types
Load loop matrices and stats
Aggregate peak analysis of differential loops
Correlation between loop and other modalities
Plot correlation between loop and mC/ATAC/RNA
Differential domain boundaries
Domain boundary prob
Domain count and size
Differential boundary
Correlation between boundary and other modalities
Plot correlation between boundary and mC/ATAC/RNA
Differential compartments
Call compartment
Compare compartment with comethylation
Plot example
Differential compartment calling with dcHiC
Correlation between compartment and other modalities
Plot correlation between compartment and mC/ATAC/RNA
Correlation Summary
Plot examples
COMMAND LINE TOOLS
hicluster filter-contact
hicluster prepare-impute
hicluster contact-distance
hicluster embedding
hicluster cpg-ratio
hicluster compartment
hicluster domain
hicluster gene-score
hicluster merge-cell-raw
hicluster merge-cool
Repository
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.rst
.pdf
comp_cpg_cell
Contents
Module Contents
comp_cpg_cell()
comp_cpg_cell
#
Module Contents
#
comp_cpg_cell
(
indir
,
outdir
,
cell
,
chrom
,
mode
,
cpg_file
)
[source]
#
Contents
Module Contents
comp_cpg_cell()