├── .DS_Store ├── .RData ├── .Rhistory ├── .gitattributes ├── .gitignore ├── README.md ├── bulkRNAseq.Rproj ├── data ├── GSE63310 │ └── GSE63310_RAW.tar ├── GSM1545535_10_6_5_11.txt ├── GSM1545536_9_6_5_11.txt ├── GSM1545537_mo906111-1_m09611-2.txt.gz ├── GSM1545538_purep53.txt ├── GSM1545539_JMS8-2.txt ├── GSM1545540_JMS8-3.txt ├── GSM1545541_JMS8-4.txt ├── GSM1545542_JMS8-5.txt ├── GSM1545543_JMS9-CDBG.txt.gz ├── GSM1545544_JMS9-P7c.txt └── GSM1545545_JMS9-P8c.txt ├── notebooks ├── 10_enrichment.Rmd ├── 1_install_packages.Rmd ├── 2_downloadRNAseq.Rmd ├── 3_annotate.Rmd ├── 4_cpm_n_log2cpm.Rmd ├── 5_filter_n_plot.Rmd ├── 6_norm_n_plot.Rmd ├── 7_unsupervised_clust.Rmd ├── 8_diff_expr.Rmd └── 9_RNA_data_viz.Rmd └── results ├── DEresults.txt ├── MDSplot-unnormalized.png ├── MDSplot.png ├── barplot_react.png ├── basal_lp_volcano.png ├── basal_ml_volcano.png ├── dotplot_react.png ├── heatmap.png └── lp_ml_volcano.png /.DS_Store: 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