padma
This is the released version of padma; for the devel version, see padma.
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Bioconductor version: Release (3.23)
Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.
Author: Andrea Rau [cre, aut]
, Regina Manansala [aut], Florence Jaffrézic [ctb], Denis Laloë [aut], Paul Auer [aut]
Maintainer: Andrea Rau <andrea.rau at inrae.fr>
citation("padma")):
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("padma")
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("padma")| padma package:Quick-start guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BioCarta, GeneExpression, MethylSeq, Pathways, PrincipalComponent, RNASeq, Software, StatisticalMethod |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL (>=3) |
| Depends | R (>= 4.1.0), SummarizedExperiment, S4Vectors |
| Imports | FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils |
| System Requirements | |
| URL | https://github.com/andreamrau/padma |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2 |
| 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 | padma_1.22.0.tar.gz |
| Windows Binary (x86_64) | padma_1.22.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | padma_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | padma_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/padma |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/padma |
| Bioc Package Browser | https://code.bioconductor.org/browse/padma/ |
| Package Short Url | https://bioconductor.org/packages/padma/ |
| Package Downloads Report | Download Stats |