karioCaS
This is the development version of karioCaS; to use it, please install the devel version of Bioconductor.
Kraken Confidence Scores for Reliable Domain-Specific Microbiota Inference and Discovery
Bioconductor version: Development (3.24)
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.
Author: Thiago Parente [aut, cre] 
, Fiocruz [fnd], IOC-Fiocruz [fnd], CAPES [fnd]
Maintainer: Thiago Parente <thiago.parente at fiocruz.br>
citation("karioCaS")):Thiago Parente. karioCaS: Kraken Confidence Scores for Reliable Domain-Specific Microbiota Inference and Discovery. doi:10.18129/B9.bioc.karioCaS, R package version 0.99.16, https://bioconductor.org/packages/karioCaS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("karioCaS")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("karioCaS")| karioCaS: Kraken Confidence Scores Exploration | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DataImport, Metagenomics, Microbiome, Software |
| Version | 0.99.16 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5.0) |
| Imports | ggplot2, patchwork, UpSetR, dplyr, readr, stringr, tidyr, scales, ggtext, SummarizedExperiment, TreeSummarizedExperiment, S4Vectors, forcats, tibble, methods, rlang, grid, grDevices, stats, utils |
| System Requirements | |
| URL | https://github.com/thiagoparentefiocruz/karioCaS |
| Bug Reports | https://github.com/thiagoparentefiocruz/karioCaS/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/karioCaS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/karioCaS |
| Package Short Url | https://bioconductor.org/packages/karioCaS/ |
| Package Downloads Report | Download Stats |