Introduction | karioCaS and Bioconductor | Installation | Input data and project folder | Importing the reports | Analysis results: the kariocas_result object | Objective thresholds | Confidence Score: the Stability Index | Minimum reads: saturation analysis | The final mosaic | Visual exploration | Taxa persistence across CS | Relative abundance heatmaps | Taxonomic resolution | Core and unique taxa across samples | Acknowledgements | Session information
Package: karioCaS 0.99.16
Thiago Parente
karioCaS: Kraken Confidence Scores for Reliable Domain-Specific Microbiota Inference and Discovery
Provides a comprehensive framework for analyzing Kraken2 metagenomic classification using multiple confidence scores. karioCaS implements a robust comparative approach to evaluate taxonomic stability across different stringency levels, facilitating the identification of reliable microbiota components and the discovery of potentially novel or unrepresented species. A key innovation is its domain-specific analysis, separately processing Bacteria, Archaea, Eukaryota, and Viruses to ensure balanced visibility of all biological domains. Includes high-quality visualization tools for retention rates, shared taxa (Upset plots), and stability heatmaps.
Authors:
karioCaS_0.99.16.tar.gz
karioCaS_0.99.16.zip(r-4.7-any)karioCaS_0.99.16.zip(r-4.6-any)karioCaS_0.99.16.zip(r-4.5-any)
karioCaS_0.99.16.tgz(r-4.6-any)karioCaS_0.99.16.tgz(r-4.5-any)
karioCaS_0.99.16.tar.gz(r-4.7-any)karioCaS_0.99.16.tar.gz(r-4.6-any)
karioCaS_0.99.16.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
karioCaS/json (API)
| # Install 'karioCaS' in R: |
| install.packages('karioCaS', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thiagoparentefiocruz/kariocas/issues
metagenomicsmicrobiomedataimportsoftware
Last updated from:f2bbabd144. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 191 | ||
| linux-devel | OK | 387 | ||
| source / vignettes | OK | 326 | ||
| linux-release | OK | 340 | ||
| macos-release | OK | 264 | ||
| macos-oldrel | OK | 282 | ||
| windows-devel | OK | 358 | ||
| windows-release | OK | 342 | ||
| windows-oldrel | OK | 238 | ||
| wasm-release | OK | 177 |
Exports:group_upsetheatmaps_karioCaSimport_karioCaSkariocas_resultreads_per_taxaretrieve_selected_taxataxa_resolutiontaxa_retentionupset_kariocas
Dependencies:abindapeBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64clicliprcodetoolscommonmarkcpp11crayoncurlDelayedArraydigestdplyrfarverforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggtextgluegridExtragridtextgtablehmsIRangesisobandjpegjsonlitelabelinglambda.rlatticelazyevallifecyclelitedownmagrittrmarkdownMatrixMatrixGenericsmatrixStatsnlmepatchworkpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimenttzdbUpSetRutf8vctrsviridisLitevroomwithrxfunxml2XVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cross-Sample UpSet: Core vs Unique Taxa per Biological Group (Step 008) | group_upset |
| Generate Heatmaps of Taxa Abundance with Extinction Patterns (Step 006) | heatmaps_karioCaS |
| Import Kraken MPA Reports to TreeSummarizedExperiment (Step 001) | import_karioCaS |
| Result of a karioCaS analysis step | kariocas_result print.kariocas_result |
| Read Cutoff Saturation Analysis & Optimal Minimum Reads (Step 003) | reads_per_taxa |
| Retrieve Selected Taxa with Domain-Specific Thresholds (Step 004) | retrieve_selected_taxa |
| Generate Taxa Resolution Analysis (Step 007) | taxa_resolution |
| Run Confidence Score Retention & Optimization (Step 002) | taxa_retention |
| Generate UpSet Plots per Sample and Domain (Step 005) | upset_kariocas |
