Data from a single-cell ChIP-seq experiment against H3K4me3 active mark from two cell lines, Jurkat B cells and Ramos T cells from Grosselin et al., 2019. The count matrices, on 5kbp bins, were given to ChromSCape and the filtering parameter was set to 3% of cells active in regions and subsampled down to 150 cells per sample. After correlation filtering, the experiment is composed of respectively 51 and 55 cells from Jurkat & Ramos and 5499 5kbp-genomic bins where signal is located.
scExp - a SingleCellExperiment with 106 cells and 5499 features (genomic bins) in hg38:
The scExp is composed of :
counts and normcounts assays, PCA, UMAP, and Correlation matrix in reducedDims(scExp)
Assignation of genes to genomic bins in rowRanges(scExp)
Cluster information in colData(scExp) correlation
Hierarchical clustering dengogram in metadata$hc_cor
Consensus clustering raw data in metadata$consclust
Consensus clustering cluster-consensus and item consensus dataframes in metadata$icl
Differential analysis in metadata$diff
Gene Set Analysis in metadata$enr
1 2 3 4 5 6
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.