rporter7 / deseq2 Goto Github PK

The goal of this program is to take the output of a RNAseq pipeline, which is a count matrix, and enable the user to analyze differentially expressed genes.

Files:

• "CountMatrix_Tribolium.csv" is the csv file of gene counts output from featureCounts.
• "DESeq2_DifferentialGeneExpression.R" is an R file that contains code to analyze gene expression across samples. This file also contains tools to make a basic volcano plot, PCA, and MAPlot.
• "dsEve RNAi_PCAplot_PCAgenecontributions.R" is an R file that contains code to visualize gene contributions to the PCA.
• "Triboliumsample_PCA.png" is the PCA output of "DESeq2_DifferentialGeneExpression.R".
• "volcano_reveal.gif" is a GIF file that is the output of the "volcanoplot.R" file.
• "volcano_total.png" is one of the outputs of "volcanoplot.R".
• "volcanoplot.R" is an R file that contains the code for ggplot2 volcano plots and transitions.