# NetActivity
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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")
```
