ssPATHS
This is the released version of ssPATHS; for the devel version, see ssPATHS.
ssPATHS: Single Sample PATHway Score
Bioconductor version: Release (3.23)
This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set (pathway) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples.
Author: Natalie R. Davidson
Maintainer: Natalie R. Davidson <natalie.davidson at inf.ethz.ch>
citation("ssPATHS")):
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")
BiocManager::install("ssPATHS")
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("ssPATHS")| Using ssPATHS | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, Classification, DimensionReduction, GeneExpression, Pathways, RNASeq, Software, Transcriptomics |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0), SummarizedExperiment |
| Imports | ROCR, dml, MESS |
| System Requirements | |
| URL |
See More
| Suggests | ggplot2, testthat (>= 2.1.0) |
| 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 | ssPATHS_1.26.0.tar.gz |
| Windows Binary (x86_64) | ssPATHS_1.26.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | ssPATHS_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | ssPATHS_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ssPATHS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ssPATHS |
| Bioc Package Browser | https://code.bioconductor.org/browse/ssPATHS/ |
| Package Short Url | https://bioconductor.org/packages/ssPATHS/ |
| Package Downloads Report | Download Stats |