This pipeline includes the General workflow to find differentially expressed genes with DESeq starting from Kallisto files or Gene count tables including helpful plots.
- DEA_analysis: added Fold-change as column in results of DE_object
- fixed batch_corrected_table when using SVA
- Added boxplots to single gene plotting
- PCA looks prettier now :D
- Changed Volcano plot because it was displaying the wrong genes in red!
- Changed the PCA of the normalized counts so you can now also plot it without a shape_option
- Changed the Top_10_genes function as it calculated the wrong genes! (did not take fold-change threshold into account)
Changed the n.sv command
- Dea_analysis: now the DEgene_number data-frame displays the right names.
- DE_genes_plot now has the comparison of the conditions in the heading.
- Fold change is now also included in the results table
- Excel files with the DEgenes and their pvalues and Fold-changes can now be created automatically.
- Creating an excel file with the normalized counts
- Now you can either add a colour to the PCA under anno_colour matching a colour to each factor in colour_obj, or not by settin anno_colour=NULL
- Adjusted the Limma_batch command so you can add your column of interest here so the variance explained by this variable never gets lost.