scExp: A SingleCellExperiment outputed by ChromSCape

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

A SingleCellExperiment outputed by ChromSCape

Description

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.

Usage

data("scExp")

Format

scExp - a SingleCellExperiment with 106 cells and 5499 features (genomic bins) in hg38:

chr

A SingleCellExperiment

Details

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

Examples

data("scExp")
plot_reduced_dim_scExp(scExp)
plot_reduced_dim_scExp(scExp,color_by = "cell_cluster")
plot_heatmap_scExp(scExp)
plot_differential_volcano_scExp(scExp,  "C1")
plot_differential_summary_scExp(scExp)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.