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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | R Script |
| Reference Manual |
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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | karioCaS_0.99.16.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | karioCaS_0.99.16.tgz |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/karioCaS/ |
| Package Short Url | https://bioconductor.org/packages/karioCaS/ |
| Package Downloads Report | Download Stats |