scHiCExplorer¶
Set of programs to process, normalize, analyse and visualize single-cell Hi-C data¶
Citation¶
Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkaa220
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 |
---|---|
Demultiplexes the samples by their barcodes to one FASTQ file per samples |
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Merges all single-cell Hi-C matrices to one |
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Compute the bulk matrix out of all single-cell Hi-C matrices |
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Changes the resolution of the matrices |
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Estimates the quality of scHi-C datasets |
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Keeps / removes chromosomes / contigs / scaffolds of all samples |
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Normalizes the read coverage of all samples to the lowest read coverage |
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Corrects all samples with Knight-Ruiz correction |
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Retrieve information about the mcool matrix |
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Cluster all samples on raw data or uses dimension reduction knn or pca |
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Cluster all samples on knn computed by approximate knn search via LSH |
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Cluster all samples based on short vs long range contact ratio |
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Cluster all samples based on A / B scHicClusterCompartments |
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Computes the consensus matrices based on clustering |
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Plots the cluster profiles with all samples |
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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
Contents:¶
This tool suite is developed by Joachim Wolff from the Bioinformatics Lab of the Albert-Ludwigs-University Freiburg, Germany.