Files contain here are the data and scripts for RNA-seq analysis workshop in BioinforSummer 4 Dec 2019
Presented by Dr Atefeh Taherian Fard and Huiwen Zheng, Australian Institute for Bioengineering and Nanotechnology, The University Of Queensland
In this workshop, you will learn how to analyse and explore RNA-seq count data. This hands-on workshop will cover basic steps in gene expression data analysis, including quality assessment, normalisation, differential gene expression testing, pathway over-representation analysis and visualisation. By the end of this workshop, you will be able to utilise the analysis workflow for your own RNA-seq data
Keywords: R, RStudio, RNA-seq, differential expression, data visualisation, DESeq2 and pathway analysis
Requirements: Participants must bring their own laptop and make sure that it has the latest version of R and RStudio installed. Experience in using R and RStudio is desired but not required.
Relevance: This workshop is relevant to anyone who is interested in learning how to present RNA-seq data in an informative and engaging way, or applying different statistical methods, to understand the data and interpret the result using R.
The example dataset used in the workshop can be found here: Craciun FL, Bijol V, Ajay AK, et al.
Download the following files from the data folder:
- Count_matrix.csv
- Metadata.csv
Note: Please download the following files and place them in your./data directory.
- Loading gene expression data into the R environment
- Identifying and filtering lowly expressed genes
- Differential gene expression analysis
- Exploration of the DE genes
- Data transformation for clustering and visualisation purposes
- Pathway over-representation analysis