Package: progeny 1.29.0

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]

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progeny.pdf |progeny.html✨
progeny/json (API)
NEWS

# 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-1.29.0(bioc 3.21)progeny-1.28.0(bioc 3.20)

systemsbiology geneexpression functionalprediction generegulation

8.91 score 93 stars 1 packages 245 scripts 903 downloads 5 exports 55 dependencies

Last updated 2 months agofrom:22fe492382. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 08 2024
R-4.5-win	NOTE	Dec 08 2024
R-4.5-linux	NOTE	Dec 08 2024
R-4.4-win	NOTE	Dec 08 2024
R-4.4-mac	NOTE	Dec 08 2024
R-4.3-win	NOTE	Dec 08 2024
R-4.3-mac	NOTE	Dec 08 2024

Exports:getModel progeny progenyPerm progenyScatter saveProgenyPlots

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

PROGENy pathway signatures

Pau Badia-i-Mompel

Rendered fromprogeny.Rmdusingknitr::rmarkdownon Dec 08 2024.

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