# Pathway RespOnsive GENes for activity inference from gene expression

## Documentation for package ‘progeny’ version 1.9.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

getModel | Returns the Progeny Model
model_human_full | The full human linear model underlying PROGENy
model_mouse_full | The full mouse linear model underlying PROGENy
progeny | Calculate PROGENy pathway scores from gene expression
progenyPerm | This function is designed to compute progeny pathway scores and assesses their significance using a gene sampling-based permutation strategy, for a series of experimental samples/contrasts.
progenyScatter | Calculate Progeny Scores with Permutations
saveProgenyPlots | Function to save Progeny plots