README

• 1 0. Install the package
• 2 1. Simplified GEO microarray workflow
• 3 2. Common small utilities
• 4 3. Download GEO-provided RNA-seq count data
• 5 4. Expression matrix conversion
  • 5.1 4.1 trans_array
  • 5.2 4.2 trans_exp_new
  • 5.3 4.3 trans_ensembl_exp
  • 5.4 4.4 trans_entrezexp
  • 5.5 4.5 TCGA grouping
• 6 5. Common plots
  • 6.1 5.1 Volcano plot
  • 6.2 5.2 PCA, tSNE, heatmap, and Venn
  • 6.3 5.3 Boxplots and correlation plots
  • 6.4 5.4 Combined plots
• 7 6. Survival analysis
• 8 7. Network and statistics utilities
• 9 8. Enrichment analysis
• 10 9. Updates
  • 10.1 9.1 New functions
  • 10.2 9.2 Function updates

✍️ Author: Xiaojie Sun