Bioconductor Code: 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](https://bioconductor.org/) with: ``` r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("NetActivity") ``` You can install the development version of NetActivity from [GitHub](https://github.com/) with: ``` r # 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: ``` r 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") ```