scHiCExplorer

Set of programs to process, normalize, analyse and visualize single-cell Hi-C data

Availability

scHiCExplorer is available as a command line suite of tools on this GitHub repository. scHiCExplorer is a general use single-cell Hi-C analysis software, to process raw single-cell Hi-C data we provide a demultiplexing tool for data provided by Nagano 2017. For all other protocols the pre-processing (demultiplexing, trimming) must be computed by third party tools. However, as long as per cell one forward and reverse mapped BAM/SAM file is provided, scHiCExplorer is able to process it.

The following is the list of tools available in scHiCExplorer

tool

description

scHicDemultiplex

Demultiplexes the samples by their barcodes to one FASTQ file per samples

scHicMergeToSCool

Merges all single-cell Hi-C matrices to one

scHicCreateBulkMatrix

Compute the bulk matrix out of all single-cell Hi-C matrices

scHicMergeMatrixBins

Changes the resolution of the matrices

scHicQualityControl

Estimates the quality of scHi-C datasets

scHicAdjustMatrix

Keeps / removes chromosomes / contigs / scaffolds of all samples

scHicNormalize

Normalizes the read coverage of all samples to the lowest read coverage

scHicCorrectMatrices

Corrects all samples with Knight-Ruiz correction

scHicInfo

Retrieve information about the mcool matrix

scHicCluster

Cluster all samples on raw data or uses dimension reduction knn or pca

scHicClusterMinHash

Cluster all samples on knn computed by approximate knn search via LSH

scHicQualityControl

Cluster all samples based on short vs long range contact ratio

scHicClusterCompartments

Cluster all samples based on A / B scHicClusterCompartments

scHicConsensusMatrices

Computes the consensus matrices based on clustering

scHicPlotClusterProfiles

Plots the cluster profiles with all samples

scHicPlotConsensusMatrices

Estimates the quality of Hi-C dataset

Getting Help

  • For all kind of questions, suggesting changes/enhancements and to report bugs, please create an issue on our GitHub repository