In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(rrrSingleCellUtils)

Multiomics data with two species, selecting human

multiomics_hg19 <-
    tenx_load_qc(h5_file = "/home/gdrobertslab/lab/Counts/S0150/filtered_feature_bc_matrix.h5",
                 species_pattern = "^hg19-",
                 exp_type = "GEX+ATAC")

multiomics_hg19

Seurat::DefaultAssay(multiomics_hg19) <- "ATAC"
multiomics_hg19 <-
    annotate_atac(multiomics_hg19,
                  "/home/gdrobertslab/lab/GenRef/10x-human_arc/genes/genes.gtf")

Nucleosome signal

multiomics_hg19 <- add_nucleosome_signal(multiomics_hg19)

Transcription start site enrichment

multiomics_hg19 <- tss_enrichment(multiomics_hg19)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.