CrcBiomeScreen
This is the development version of CrcBiomeScreen; to use it, please install the devel version of Bioconductor.
An R package for colorectal cancer screening and microbiome analysis
Bioconductor version: Development (3.23)
A developed and benchmarked reproducible machine learning framework for microbiome-based colorectal cancer (CRC) screening. By systematically evaluating normalization strategies, taxonomic resolutions, and class imbalance handling. This R package allows users to apply the full pipeline or selectively run specific components depending on their analytical needs. It establishes a scalable foundation for developing interpretable microbiome-based screening tools to support early CRC detection. This approach could be easily implemented in a national screening programme, to improve early detection rates for this disease.
Author: Chengxin Li [cre, aut]
, Rishabh Bezbaruah [aut], Henry Wood [aut], Arief Gusnanto [aut]
Maintainer: Chengxin Li <ngzh5554 at leeds.ac.uk>
citation("CrcBiomeScreen")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("CrcBiomeScreen")
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("CrcBiomeScreen")| CrcBiomeScreen | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, Metagenomics, Microbiome, Normalization, Software, Visualization |
| Version | 0.99.15 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | rlang, methods, dplyr, doFuture, doParallel, foreach, future, future.apply, pROC, progress, progressr, stats, tibble, tidyr, TreeSummarizedExperiment, ggplot2, GUniFrac, magrittr, parallel, withr, SummarizedExperiment, caret, ranger, utils, graphics, grDevices |
| System Requirements | |
| URL | https://github.com/omicsForestry/CrcBiomeScreen |
| Bug Reports | https://github.com/omicsForestry/CrcBiomeScreen/issues |
See More
| Suggests | rstatix, MASS, mgcv, ggplotify, ggpubr, ggrepel, ggtree, glmnet, Matrix, microbiome, phyloseq, vegan, gt, testthat (>= 3.0.0), BiocManager, devtools, knitr, rmarkdown, BiocStyle, curatedMetagenomicData, xgboost |
| 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 | CrcBiomeScreen_0.99.15.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | CrcBiomeScreen_0.99.15.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CrcBiomeScreen |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CrcBiomeScreen |
| Bioc Package Browser | https://code.bioconductor.org/browse/CrcBiomeScreen/ |
| Package Short Url | https://bioconductor.org/packages/CrcBiomeScreen/ |
| Package Downloads Report | Download Stats |