Package index • SCEGHiC

Preprocess data

process_data(): Create preprocessed input data for SCEG-HiC

Aggregate_datasets(): Create aggregated data for SCEG-HiC

generate_aggregated_datasets(): Create aggregated data for a certain cluster

estimateSizeFactorsForMatrix(): Function to calculate the size factor for the single-cell data

asSlamMatrix(): Convert a sparseMatrix from Matrix package to a slam matrix

isSparseMatrix(): Convert a sparseMatrix from Matrix package to a slam matrix

estimateSizeFactorsForSparseMatrix(): Estimate size factors for each column, given a sparseMatrix from the Matrix package

estimateSizeFactorsForDenseMatrix(): Estimate size factors dense matrix

estimate_t(): Find the most commonly occuring relative expression value in each cell

dmode(): use gaussian kernel to calculate the mode of transcript counts

Calculate weight

calculateHiCWeights(): Calculate promoters, enhancers, and Hi-C matrix for genes

annotateTSS(): Annotate transcription start sites (TSS)

liftOverPeaks(): Convert genomic coordinates of peaks between genome assemblies

Run model

Run_SCEG_HiC(): Run the SCEG-HiC Model

normalizeHiCWeights(): Normalize the bulk average Hi-C matrix

wglasso(): Gene network reconstruction using prior biological knowledge

Visualize the gene-enhancer

connections_Plot(): Plot SCEG-HiC predicted enhancer-gene links

coverPlot(): Plot SCEG-HiC Links and Tn5 Insertion Frequency Over a Genomic Region

LinksPlot(): Plot linked genomic elements

data

hg19TSSdata: hg19TSSdata

hg38TSSdata: hg38TSSdata

mm10TSSdata: mm10TSSdata

mm9TSSdata: mm9TSSdata

multiomic_small: A small example paired scRNA-seq and scATAC-seq data.