README.md

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

Roberts Lab R Single Cell Analysis Utility functions

These are utility functions for use by the Roberts lab to analyze single cell sequencing data.

Functions

Working and tested functions

• tenx_load_qc()
  • Load 10X data
  • Formerly tenXLoadQC()
  • Now requires mt_pattern and species_pattern instead of spec
• gen_cellecta_bc_data()
  • Extract cellecta barcode information from a sam or bam file
• plot_complex_heatmap()
  • Make a complex heatmap showing nichenet output from FindLigands()
• find_ligands()
  • Formerly findLigands()
  • Run nichenetr to find ligands potentially inducing receptor-driven gene expression changes
• find_tar_genes()
  • Formerly findTarGenes()
  • Create a gene list containing putative targets of ligand activity
• kill_cc()
  • Formerly killCC()
  • Regress out cell cycle effects
• plot_cc()
  • Plot the proportion of cells in each cell cycle stage

Still in testing

• process_ltbc()

To do

• Make arguments inherit documentation from other functions instead of re-typing them
• Add argument to provide path to cellranger
• Vignette
• For multiomics, make sure both atac and gex are present in sample input sheet, and not as "sample1_atac" and "sample1_gex", which will fail. Should be "sample1" and "sample1" for both.
• Try out snp calling: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1863-4
• In tenx_load_qc, check if all data is filtered out or sobj is empty
• Figure out multiomic FRiP calculation and see if I need to divide by 2
  • https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/algorithms/overview
• Make optimize_silhouette warn if there are no dim reductions or clustering present
• Try out snp calling: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1863-4
• In tenx_load_qc, check if all data is filtered out or sobj is empty

Errors

If you run into any errors, please run the following commands and send the output to me along with the error messages produced.

traceback() sessionInfo()

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