# Analysis and Exploration of Mixed Microbial Genomic Samples

## Documentation for package ‘MixviR’ version 3.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_depths_to_ref | Add Read Depths To Ref
call_mutations | Identify Variants From A Potentially Mixed Sample
create_ref | Create MixVir-formatted reference genome object
estimate_lineages | Estimate Lineage Proportions In Samples
explore_mutations | MixviR Shiny Dashboard
get_codons | Get Codons From Gene Sequence
id_indels | ID Indel-based Amino Acid Changes
id_snps | ID SNV-based Amino Acid Changes
vcf_to_mixvir | Convert Sample VCF to MixviR Input Format