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Makefile
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.PHONY: clean
clean:
rm -rf figures
rm -rf .created-dirs
rm -f report.pdf
rm -f report.html
rm -f report.tex
rm -f report.log
rm -f Rplots.pdf
.created-dirs:
mkdir -p figures
touch .created-dirs
# RNA QC + RNA processing
# Build UMAP on RNA with resolution = 0.5 for clustering
~/work/figures/UMAP_RNA0.5.png\
~/work/figures/UMAP_RNA0.5.rds\
~/work/Data/Cov2RNA_clustered.rds\
~/work/figures/violin_RNA_QC.rds: .created-dirs ~/work/Data/cov02
Rscript RNA_processing.R
# RNA violin plots for each cluster on given DE genes
~/work/figures/RNA_violin_T.rds\
~/work/figures/RNA_violin_T4_T8.rds\
~/work/figures/RNA_violin_B.rds\
~/work/figures/RNA_violin_NK.rds\
~/work/figures/RNA_violin_CD14mono.rds\
~/work/figures/RNA_violin_DC.rds\
~/work/figures/RNA_violin_PL.rds: .created-dirs ~/work/Data/Cov2RNA_clustered.rds
Rscript RNA_cluster_violin_plots.R
# RNA DE analysis for each cluster using Wilcoxon rank sum test
~/work/figures/RNA_DEcluster_heatmap.rds: .created-dirs ~/work/Data/Cov2RNA_clustered.rds
Rscript RNA_DE_Wilcoxon.R
# Explore ADT
~/work/figures/ADT_hist_CD3.rds\
~/work/figures/RNA_hist_CD3.rds\
~/work/Data/ADT_10sample.rds: .created-dirs ~/work/Data/Cov2RNA_clustered.rds
Rscript ADT_explore.R
# Processing ADT
~/work/Data/ADT_10sample_normalzied.rds\
~/work/figures/ADT_violin_T.rds\
~/work/figures/ADT_violin_T4_T8.rds\
~/work/figures/ADT_violin_T4naive.rds\
~/work/figures/ADT_violin_T4memeff.rds\
~/work/figures/ADT_violin_B.rds\
~/work/figures/ADT_violin_NK.rds\
~/work/figures/ADT_violin_CD14mono.rds\
~/work/figures/ADT_violin_CD14mono.rds: .created-dirs ~/work/Data/Cov2RNA_clustered.rds
Rscript ADT_processing.R
# Build report
report.html: .created-dirs ~/work/figures/UMAP_RNA0.5.rds\
~/work/figures/violin_RNA_QC.rds\
~/work/figures/RNA_violin_T.rds\
~/work/figures/RNA_violin_T4_T8.rds\
~/work/figures/RNA_violin_B.rds\
~/work/figures/RNA_violin_NK.rds\
~/work/figures/RNA_violin_CD14mono.rds\
~/work/figures/RNA_violin_DC.rds\
~/work/figures/RNA_DEcluster_heatmap.rds\
~/work/figures/ADT_hist_CD3.rds\
~/work/figures/RNA_hist_CD3.rds\
~/work/Data/ADT_10sample.rds\
~/work/Data/ADT_10sample_normalzied.rds\
~/work/figures/ADT_violin_T.rds\
~/work/figures/ADT_violin_T4_T8.rds\
~/work/figures/ADT_violin_T4naive.rds\
~/work/figures/ADT_violin_T4memeff.rds\
~/work/figures/ADT_violin_B.rds\
~/work/figures/ADT_violin_NK.rds\
~/work/figures/ADT_violin_CD14mono.rds\
~/work/figures/ADT_violin_DC.rds\
~/work/UMAP_celltypeRNA.png\
~/work/UMAP_celltypeADT.png
R -e "rmarkdown::render(\"report.Rmd\", output_format=\"html_document\")"