scHiCExplorer tools

tool	type	input files	main output file(s)	application
scHicDemultiplex	preprocessing	1 FASTQ file SRR to sample mapping file Barcode file	2*n demultiplexed FASTQ files	Demultiplexes the samples by their barcodes to one FASTQ file per samples
scHicMergeToSCool	preprocessing	n Hi-C matrices in cool format	One scool file containg all Hi-C matrices	Merges all single-cell Hi-C matrices to one
scHicManageScool	preprocessing	scool Hi-C matrix	one scool matrix or cool matrix	update old version 4 of scHiCExplorer scool file to new scool file of version 5
scHicConvertFormat	preprocessing	scool Hi-C matrix	scHiCluster data	Converts scool to scHiCluster files
scHicMergeMatrixBins	preprocessing	scool Hi-C matrix	scool Hi-C matrix	Changes the resolution of the matrices
scHicQualityControl	preprocessing	scool Hi-C matrix	One scool file, two qc images, qc report	Checks the quality of all samples and removes bad ones
scHicAdjustMatrix	preprocessing	scool Hi-C matrix	scool Hi-C matrix	Keeps / removes chromosomes / contigs / scaffolds of all samples
scHicNormalize	preprocessing	scool Hi-C matrix	scool Hi-C matrix	Normalizes the read coverage of all samples to the lowest read coverage
scHicCorrectMatrices	preprocessing	scool Hi-C matrix	scool Hi-C matrix	Corrects all samples with Knight-Ruiz correction
scHicInfo	information	scool Hi-C matrix	information about the scool matrix	Retrieve information about the scool matrix: resolution, number of samples, etc
scHicCreateBulkMatrix	analysis	scool Hi-C matrix	cool Hi-C matrix	Changes the resolution of the matrices
scHicCluster	analysis	scool Hi-C matrix	text file with sample to cluster association	Cluster all samples on raw data or uses dimension reduction knn or pca
scHicClusterMinHash	analysis	scool Hi-C matrix	text file with sample to cluster association	Cluster all samples on knn computed by approximate knn search via LSH
scHicQualityControl	analysis	scool Hi-C matrix	text file with sample to cluster association	Cluster all samples based on short vs long range contact ratio
scHicClusterCompartments	analysis	scool Hi-C matrix (gene or histone track)	text file with sample to cluster association	Cluster all samples based on A / B scHicClusterCompartments
scHicConsensusMatrices	analysis	scool Hi-C matrix, txt file sample to cluster association	scool Hi-C matrix with consensus matrices	Computes the consensus matrices based on clustering
scHicPlotClusterProfiles	visualization	scool Hi-C matrix txt file sample to cluster association	one image with cluster profiles	Plots the cluster profiles with all samples
scHicPlotConsensusMatrices	visualization	scool Hi-C matrix txt file sample to cluster association	one image with consensus matrices	Plots the cluster consensus matrices

General principles

A typical scHiCExplorer command could look like this:

$ scHicPlotClusterProfiles -m matrix.scool \
-o cluster_profiles.png \
-c computed_clusters.txt \
--dpi 300

You can always see all available command-line options via –help:

$ scHicInfo -m matrix.scool

Tools for demultiplexing of raw fastq files

scHicDemultiplex

Tools for single-cell Hi-C data pre-preprocessing

scHicAdjustMatrix

scHicCorrectMatrices

scHicMergeMatrixBins

scHicMergeToSCool

scHicNormalize

scHicManageScool

scHicConvertFormat

Tools for information about the single-cell Hi-C matrix

scHicInfo

Tools for single-cell Hi-C QC

scHicQualityControl

Tools for Hi-C data analysis

scHicCluster

scHicClusterCompartments

scHicClusterMinHash

scHicQualityControl

scHicConsensusMatrices

Tools for single-cell Hi-C visualization

scHicPlotClusterProfiles

scHicPlotConsensusMatrices