progeny
This is the released version of progeny; for the devel version, see progeny.
Pathway RespOnsive GENes for activity inference from gene expression
Bioconductor version: Release (3.23)
PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.
Author: Michael Schubert [aut], Alberto Valdeolivas [ctb]
, Christian H. Holland [ctb]
, Igor Bulanov [ctb], Aurélien Dugourd [cre, ctb]
Maintainer: Aurélien Dugourd <aurelien.dugourd at bioquant.uni-heidelberg.de>
citation("progeny")):
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("progeny")
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("progeny")| PROGENy pathway signatures | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FunctionalPrediction, GeneExpression, GeneRegulation, Software, SystemsBiology |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | Apache License (== 2.0) | file LICENSE |
| Depends | R (>= 3.6.0) |
| Imports | Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra, decoupleR, reshape2 |
| System Requirements | |
| URL | https://github.com/saezlab/progeny |
| Bug Reports | https://github.com/saezlab/progeny/issues |
See More
| Suggests | airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | easier |
| Suggests Me | autonomics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | progeny_1.34.0.tar.gz |
| Windows Binary (x86_64) | progeny_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | progeny_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | progeny_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/progeny |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/progeny |
| Bioc Package Browser | https://code.bioconductor.org/browse/progeny/ |
| Package Short Url | https://bioconductor.org/packages/progeny/ |
| Package Downloads Report | Download Stats |