Package: progeny 1.27.0
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:
progeny_1.27.0.tar.gz
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progeny_1.27.0.tgz(r-4.4-any)progeny_1.27.0.tgz(r-4.3-any)
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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
- 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-1.27.0(bioc 3.20)progeny-1.26.0(bioc 3.19)
Last updated 2 months agofrom:26fbffdfe9
Exports:getModelprogenyprogenyPermprogenyScattersaveProgenyPlots
Dependencies:backportsBHBiobaseBiocGenericsBiocParallelbroomclicodetoolscolorspacecpp11decoupleRdplyrfansifarverformatRfutile.loggerfutile.optionsgenericsggplot2ggrepelgluegridExtragtableisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangscalessnowstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
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 |