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MixviR  

Analysis and Exploration of Mixed Microbial Genomic Samples
View on CRAN: Click here


Download and install MixviR package within the R console
Install from CRAN:
install.packages("MixviR")

Install from Github:
library("remotes")
install_github("cran/MixviR")

Install by package version:
library("remotes")
install_version("MixviR", "3.5.0")



Attach the package and use:
library("MixviR")
Maintained by
Michael Sovic
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-05-04
Latest Update: 2022-10-22
Description:
Tool for exploring DNA and amino acid variation and inferring the presence of target lineages from microbial high-throughput genomic DNA samples that potentially contain mixtures of variants/lineages. MixviR was originally created to help analyze environmental SARS-CoV-2/Covid-19 samples from environmental sources such as wastewater or dust, but can be applied to any microbial group. Inputs include reference genome information in commonly-used file formats (fasta, bed) and one or more variant call format (VCF) files, which can be generated with programs such as Illumina's DRAGEN, the Genome Analysis Toolkit, or bcftools. See DePristo et al (2011) and Danecek et al (2021) for these tools, respectively. Available outputs include a table of mutations observed in the sample(s), estimates of proportions of target lineages in the sample(s), and an R Shiny dashboard to interactively explore the data.
How to cite:
Michael Sovic (2022). MixviR: Analysis and Exploration of Mixed Microbial Genomic Samples. R package version 3.5.0, https://cran.r-project.org/web/packages/MixviR
Previous versions and publish date:
3.3.5 (2022-05-04 09:20)
Other packages that cited MixviR R package
View MixviR citation profile
Other R packages that MixviR depends, imports, suggests or enhances
Functions, R codes and Examples using the MixviR R package
Some associated functions: add_depths_to_ref . call_mutations . create_ref . estimate_lineages . explore_mutations . get_codons . id_indels . id_snps . vcf_to_mixvir . 
Some associated R codes: RGlobals.R . app.R . create_ref.R . estimate_lineages.R . get_codons.R . id_mutations.R .  Full MixviR package functions and examples
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