A beginner's guide to creating a bulkAnalyseR app from a GEO dataset"

wzxhzdk:0 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: wzxhzdk:1 ## 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. wzxhzdk:2 wzxhzdk:3 ### 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. wzxhzdk:4 ### Pre-processing We can now denoise and normalise the data using bulkAnalyseR wzxhzdk:5 ### 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/). wzxhzdk:6 wzxhzdk:7

Try the bulkAnalyseR package in your browser

Any scripts or data that you put into this service are public.

bulkAnalyseR documentation built on Dec. 28, 2022, 2:04 a.m.