Package: MixviR 3.5.0
MixviR: Analysis and Exploration of Mixed Microbial Genomic Samples
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) <doi:10.1038/ng.806> and Danecek et al (2021) <doi:10.1093/gigascience/giab008> 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.
Authors:
MixviR_3.5.0.tar.gz
MixviR_3.5.0.zip(r-4.5)MixviR_3.5.0.zip(r-4.4)MixviR_3.5.0.zip(r-4.3)
MixviR_3.5.0.tgz(r-4.4-any)MixviR_3.5.0.tgz(r-4.3-any)
MixviR_3.5.0.tar.gz(r-4.5-noble)MixviR_3.5.0.tar.gz(r-4.4-noble)
MixviR_3.5.0.tgz(r-4.4-emscripten)MixviR_3.5.0.tgz(r-4.3-emscripten)
MixviR.pdf |MixviR.html✨
MixviR/json (API)
NEWS
| # Install 'MixviR' in R: |
| install.packages('MixviR', repos = c('https://mikesovic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mikesovic/mixvir/issues
Last updated 2 years agofrom:6c4cf2e6e7. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-win | OK | Oct 29 2024 |
| R-4.5-linux | OK | Oct 29 2024 |
| R-4.4-win | OK | Oct 29 2024 |
| R-4.4-mac | OK | Oct 29 2024 |
| R-4.3-win | OK | Oct 29 2024 |
| R-4.3-mac | OK | Oct 29 2024 |
Exports:add_depths_to_refcall_mutationscreate_refestimate_lineagesexplore_mutationsget_codonsid_indelsid_snpsvcf_to_mixvir
Dependencies:apeaskpassbase64encBiocGenericsBiostringsbitbit64bslibcachemclicliprclustercolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisememusemgcvmimemunsellnlmeopensslpermutepillarpinfsc50pkgconfigplotlyprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownS4VectorssassscalesshinysourcetoolsstringistringrsystibbletidyrtidyselecttimechangetinytextzdbUCSC.utilsutf8vcfRvctrsveganviridisLitevroomwithrxfunxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add Read Depths To Ref | add_depths_to_ref |
| Identify Variants From A Potentially Mixed Sample | call_mutations |
| Create MixVir-formatted reference genome object | create_ref |
| Estimate Lineage Proportions In Samples | estimate_lineages |
| MixviR Shiny Dashboard | explore_mutations |
| Get Codons From Gene Sequence | get_codons |
| ID Indel-based Amino Acid Changes | id_indels |
| ID SNV-based Amino Acid Changes | id_snps |
| Convert Sample VCF to MixviR Input Format | vcf_to_mixvir |
