Tag: r
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RNA-Seq Analysis in WSL – Part 3 : Differential expression analysis using Ballgown
Once we create the transcript abundance data using Stringtie, we can now perform the differential expression analysis. With Strigtie, we had created the estimated transcript abundance data which is compatible with Ballgown. The directory structure of the `for_ballgown` directory looks like this: To perform the differential gene expression analyis open Rstudio and change working directory…
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RNA-Seq Analysis in WSL – Part 1 : Installation of tools
In this series of posts, we will see how we can perform RNA-Seq analysis in Windows operating system using linux tools in WSL. Also, the part of analysis which require “R”, will be done in the Windows system. We will be using following tools: Install samtools We need to install three things for this. Open…
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How to plot metabolite concentrations in R?
The data source Let’s say we have the final concentrations of following metabolites from three strains of bacteria: Each strain was grown in triplicates, so we have three values of each metabolite for each strain. Load tidyverse We will first load the tidyverse library which contains all the functions that we are going to need here. Read data…