ClustAll
This is the development version of ClustAll; for the stable release version, see ClustAll.
ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases
Bioconductor version: Development (3.24)
Data driven strategy to find hidden groups of patients with complex diseases using clinical data. ClustAll facilitates the unsupervised identification of multiple robust stratifications. ClustAll, is able to overcome the most common limitations found when dealing with clinical data (missing values, correlated data, mixed data types).
Author: Asier Ortega-Legarreta [aut, cre]
, Sara Palomino-Echeverria [aut]
Maintainer: Asier Ortega-Legarreta <aortegal at navarra.es>
citation("ClustAll")):
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("ClustAll")
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("ClustAll")| ClustALL User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DimensionReduction, PrincipalComponent, Software, StatisticalMethod |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.2.0) |
| Imports | FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 |
| 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 | ClustAll_1.9.0.tar.gz |
| Windows Binary (x86_64) | ClustAll_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | ClustAll_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | ClustAll_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ClustAll |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ClustAll |
| Bioc Package Browser | https://code.bioconductor.org/browse/ClustAll/ |
| Package Short Url | https://bioconductor.org/packages/ClustAll/ |
| Package Downloads Report | Download Stats |