# Single-Cell Analysis of Host-Microbiome Interactions

## Documentation for package ‘rsahmi’ version 0.0.2

- DESCRIPTION file.
- Package NEWS.

## Help Pages

blsd | Barcode level signal denoising
extractor | Extract reads and output from Kraken
extract_kraken_output | Extract reads and output from Kraken
extract_kraken_reads | Extract reads and output from Kraken
extract_taxids | Extract reads and output from Kraken
parse_kraken_report | Parse kraken report file
prep_dataset | Prepare kraken report, k-mer statistics, UMI data
read_dataset | Prepare kraken report, k-mer statistics, UMI data
remove_contaminants | Identifying contaminants and false positives taxa (cell line quantile test)
slsd | Sample level signal denoising
taxa_counts | Quantitation of microbes