GitHub - yocra3/NetActivity (original) (raw)

NetActivity

The goal of NetActivity is to compute gene set scores. Gene set scores are computed based on the weights obtained from training a sparsely-connected autoencoder.

Installation

You can install the current release version of NetActivity from Bioconductor with:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("NetActivity")

You can install the development version of NetActivity from GitHub with:

install.packages("devtools")

devtools::install_github("yocra3/NetActivity") devtools::install_github("yocra3/NetActivityData")

Example

This is a basic example which shows you how to solve a common problem:

library(NetActivity) library(airway) data(airway) ddsSE <- DESeq2::DESeqDataSet(airway, design = ~ cell + dex) vst <- DESeq2::varianceStabilizingTransformation(ddsSE) out <- prepareSummarizedExperiment(vst, "gtex_gokegg") scores <- computeGeneSetScores(out, "gtex_gokegg")