R-Ladies Tunis : RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR by Xueyi Dong

This is the 6th workshop of the #R4Bioinfo series that we've launched in September 2020. This series of workshops aims to cover various subjects related to the #bioinformatics field.

This meetup was held on Saturday, February 6, 2021 https://www.meetup.com/rladies-tunis/...

We have been hosting Xueyi Dong who animated an incredible workshop about RNA-seq.

▶️ Invited trainer : Xueyi Dong
▶️ Xueyi Dong (https://github.com/XueyiDong) :
Xueyi Dong is a PhD candidate at Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. She loves to share her experiences with RNA-seq data analysis. Xueyi has translated the analysis workflow package RNAseq123 (https://bioconductor.org/packages/rel...) into Mandarin, and she has taught the workshop on different events using both English and Mandarin.

Moderator :
Dr. Hédia Tnani : PhD on Molecular Biology and Biotechnology, Co-founder at R-Ladies Tunis https://github.com/HediaTnani

Abstract : The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential expression testing and pathway analysis with the results obtained informing future experiments and validation studies. In the following workflow article (https://f1000research.com/articles/5-..., the RNA-sequencing data are analyzed from the mouse mammary gland, demonstrating use of the popular edgeR package to import, organise, filter and normalise the data, followed by the limma package with its voom method, linear modelling and empirical Bayes moderation to assess differential expression and perform gene set testing. This pipeline is further enhanced by the Glimma package which enables interactive exploration of the results so that individual samples and genes can be examined by the user. The complete analysis offered by these three packages highlights the ease with which researchers can turn the raw counts from an RNA-sequencing experiment into biological insights using Bioconductor (https://f1000research.com/articles/5-....

The workflow that Xueyi Dong was presenting is based on the Bioconductor package RNAseq123 (https://bioconductor.org/packages/rel..., which contains all the R packages (#rstats) needed for the analysis and also the vignettes. The vignettes can also be accessed via F1000 (the workflow paper https://f1000research.com/articles/5-..., and the design matrix guide https://f1000research.com/articles/9-..., where a PDF version is available.

Slides 👉 https://drive.google.com/file/d/13DXT...

In order to review the 1st workshop, the 2nd workshop and the 3rd workshop of our R4Bioinfo series, you may follow these links 👉
🟪 1st workshop : Introduction to RNA-seq workshop animated by Dr. Michael Love    • R-Ladies Tunis (English) - Introduction to...  
🟪 2nd workshop : Introduction to Bioconductor Annotation Resources workshop by Pr. Martin Morgan    • R-Ladies Tunis (English) - Intro to Biocon...  
🟪 3rd workshop : Introduction to GenomicRanges and plyranges workshop animated by Dr. Stephanie Hicks    • R-Ladies Tunis (English) - Intro to Genomi...  
🟪 4th workshop : Introduction to Genome-Wide Association Studies (GWAS) animated by Dr. Dr. Tatiana Tatarinova    • R-Ladies Tunis : Intro to Genome-Wide Asso...  

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