Roberts Lab R Single Cell Analysis Utility functions

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

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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

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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()