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In this short tutorial we showcase a simple pipeline to create a bulkAnalyseR app using a publicly available dataset from the [Gene Expression Omnibus (GEO)](https://www.ncbi.nlm.nih.gov/geo/). No pre-requisites are required, as the installation of bulkAnalyseR and download of the data are included.
The example app described in this vignette can be found [here](https://bioinf.stemcells.cam.ac.uk/shiny/bulkAnalyseR/GEO/).
## Installation
First, install the latest version of bulkAnalyseR, starting with the CRAN and Bioconductor dependencies:
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## Download data and create app
### Get the expression matrix
We start by downloading and reading in the expression matrix. Rows represent genes/features and columns represent samples (note you need an internet connection to run the code below). The matrix is from [a 2022 study](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178620) on the Stem Cell transcriptional response to Microglia-Conditioned Media. We only use a few samples in the study for illustrative purposes.
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### Defining metadata
We use a very simple metadata table with just the main condition in the experiment. Detailed metadata is available for all GEO datasets and can be downloaded and used instead.
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### Pre-processing
We can now denoise and normalise the data using bulkAnalyseR
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### Creating the shiny app
Finally, we can create a shiny app. This example app can be found [here](https://bioinf.stemcells.cam.ac.uk/shiny/bulkAnalyseR/GEO/).
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