This Shiny app performs absolute deconvolution on RNA-Seq and microarray data. It also contain a Gene Viewer page where the expression of a gene can be visualized accorss 29 immune cell types.

You can run the apps in several ways:

This shiny app is hosted online at the https://giannimonaco.shinyapps.io/ABIS/. It does not need R installation and it can be immediately used by just clicking on the link.

We suggest using ABIS from the web only for testing. For larger analysis we encourage to install the shiny app locally.

You need to download the app from GitHub through R and it will run locally. However, as soon as you will close R, the app will not be available anymore and you need it to download it again. All the packages and dependecies need to be installed first.

install.packages(c("shiny", "MASS"), dependencies = TRUE)

runGitHub("ABIS", user="giannimonaco")

Save the repository on your local machine. Open either the ui.r or the server.R file with RStudio.

The gene expression matrix of your PBMC samples must be in a Tab delimited format. The gene names must be gene symbols.

For RNA-Seq deconvolution the gene expression values must be TPM values. RNA-Seq deconvolution has been implemented using data from Illumina HiSeq 2000.

For microarray deconvolution, the expression values should derive from the selection of the maximum expression value from the probes encoding for a single gene. Micorarray deconvolution has been implemented using data from Illumina HT-12 v4.

Please, be aware that platform and pre-processing specific effects can occur.

The Gene Viewer panel shows the median gene expression value of a gene accross the 29 immune cell types contained in our dataset. It is straitforward to use, simply enter the name of a gene in one of these formats: gene symbol, Ensembl ID or Entrez ID.

This software is released under the GPL v2 license, "which guarantees end users (individuals, organizations, companies) the freedoms to use, study, share (copy), and modify the software".