Differential gene expression using R studio
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3.9 years ago
rachana.cdri ▴ 10

Hello everyone,

I am new to r-studio and I have to do differential gene expression analysis for my RNA seq data. Please tell me how should I start.I already have read counts for my samples.

Thank you

RNA-Seq • 11k views
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Read about rnaseq here by University of Oregan. http://rnaseq.uoregon.edu/. Once RNAseq fundamentals are clear, try to reproduce this workflow as you are looking for differential gene expression: https://www.bioconductor.org/help/workflows/rnaseqGene/. R studio, as many people said here, is a R front end.

Could you update us with the method of obtaining read counts? (for eg featurecounts or htseq or any other tool).

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3.9 years ago
Ram 32k

RStudio is an interface. You're looking for software written in R (called packages) that help you with DE analysis. Packages such as DESeq2 and edgeR might be a good place to start.

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3.9 years ago

Dear Rachana,

I would suggest you to learn and understand the fundamentals of differential gene expression(DGE). Try to compile the following first :

  1. What is the objective of your study?
  2. What do you have as your data set, experimental setup, replciates, species in question, source of samples etc.
  3. Fundamentals of DGE - mapping, raw read counts, FPKM, RPKM or TPM.

A nice paper could be found here

Then, finally decide the appropriate tool; though all of them can more or less perform the basic analysis for you.

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