Package: progeny 1.35.0

Aurélien Dugourd

progeny: Pathway RespOnsive GENes for activity inference from gene expression

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.

Authors:Michael Schubert [aut], Alberto Valdeolivas [ctb], Christian H. Holland [ctb], Igor Bulanov [ctb], Aurélien Dugourd [cre, ctb]

progeny_1.35.0.tar.gz
progeny_1.35.0.zip(r-4.7-any)progeny_1.35.0.zip(r-4.6-any)progeny_1.35.0.zip(r-4.5-any)
progeny_1.35.0.tgz(r-4.6-any)progeny_1.35.0.tgz(r-4.5-any)
progeny_1.35.0.tar.gz(r-4.7-any)progeny_1.35.0.tar.gz(r-4.6-any)
progeny_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
progeny/json (API)

# Install 'progeny' in R:

install.packages('progeny', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/saezlab/progeny/issues

Datasets:

model_human_full - The full human linear model underlying PROGENy
model_mouse_full - The full mouse linear model underlying PROGENy
vignette_data - The RNA data used in the progeny vignette

On BioConductor:progeny-1.35.0(bioc 3.24)progeny-1.34.0(bioc 3.23)

systemsbiology geneexpression functionalprediction generegulation

8.98 score 130 stars 359 scripts 1.7k downloads 5 exports 50 dependencies

Last updated from:9779c69771. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	188
linux-devel	NOTE	355
source / vignettes	OK	254
linux-release	NOTE	317
macos-release	NOTE	186
macos-oldrel	NOTE	216
windows-devel	NOTE	229
windows-release	NOTE	235
windows-oldrel	NOTE	237
wasm-release	OK	151

Exports:getModel progeny progenyPerm progenyScatter saveProgenyPlots

Dependencies:backports BH Biobase BiocGenerics BiocParallel broom cli codetools cpp11 decoupleR dplyr farver formatR futile.logger futile.options generics ggplot2 ggrepel glue gridExtra gtable isoband labeling lambda.r lattice lifecycle magrittr Matrix parallelly pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp reshape2 rlang S7 scales snow stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

PROGENy pathway signatures

Introduction | Activity estimation | Load | Exploration

Rendered fromprogeny.Rmdusingknitr::rmarkdown

Last update: 2022-04-20
Started: 2017-09-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Returns the Progeny Model	getModel
The full human linear model underlying PROGENy	model_human_full
The full mouse linear model underlying PROGENy	model_mouse_full
Calculate PROGENy pathway scores from gene expression	progeny
Compute progeny pathway scores and assesses significance based on permutations	progenyPerm
Calculate Progeny Scores with Permutations	progenyScatter
Function to save Progeny plots	saveProgenyPlots
The RNA data used in the progeny vignette	vignette_data