rScudo
This is the development version of rScudo; for the stable release version, see rScudo.
Signature-based Clustering for Diagnostic Purposes
Bioconductor version: Development (3.24)
SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.
Author: Matteo Ciciani [aut, cre], Thomas Cantore [aut], Enrica Colasurdo [ctb], Mario Lauria [ctb]
Maintainer: Matteo Ciciani <matteo.ciciani at gmail.com>
citation("rScudo")):
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("rScudo")
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("rScudo")| Signature-based Clustering for Diagnostic Purposes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Classification, Clustering, DifferentialExpression, FeatureExtraction, GeneExpression, GraphAndNetwork, Network, Proteomics, Software, SystemsBiology, Transcriptomics |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics |
| System Requirements | |
| URL | https://github.com/Matteo-Ciciani/scudo |
| Bug Reports | https://github.com/Matteo-Ciciani/scudo/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel |
| 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 | rScudo_1.29.0.tar.gz |
| Windows Binary (x86_64) | rScudo_1.29.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | rScudo_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | rScudo_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rScudo |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rScudo |
| Bioc Package Browser | https://code.bioconductor.org/browse/rScudo/ |
| Package Short Url | https://bioconductor.org/packages/rScudo/ |
| Package Downloads Report | Download Stats |