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A beginner's guide to creating a bulkAnalyseR app from a GEO dataset"
In bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data
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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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bulkAnalyseR documentation built on Dec. 28, 2022, 2:04 a.m.
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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
bulkAnalyseR documentation built on Dec. 28, 2022, 2:04 a.m.
Try the bulkAnalyseR package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.