Pre-Workshop

Software Requirements

Please follow the instructions in this document

Workshop Agenda & Materials

Detailed Workshop Agenda can be found here

Day 1 Data Files

• DEGs_5_PAHs.csv
• Norm_Data_Zebrafish_Top5k_CV.csv
• Norm_Data_Zebrafish_Top500_CV_NoOutliers_RepsAv.csv
• Zebrafish_Condition_Info.csv
• Raw_Count_Data_Zebrafish.csv
• Normalized_Data_Synechococcus.csv
• Zebrafish_Condition_Info_Correct_Names.csv

Day 2 Data Files

• Norm_Data_Zebrafish_Top5k_CV_NoOutliers.csv
• Norm_Data_Zebrafish_Top5k_CV_NoOutliers_Transpose_ExpAdded.csv
• Norm_Data_Zebrafish_Retene_v_Control_ALL.csv
• Normalized_Data_Synechococcus_Transpose.csv
• graphml file
• sif file
• Normalized_Data_Synechococcus_Transpose_Unwht_9.235387_Min12_Mods.csv
• Normalized_Data_Synechococcus_Transpose_Unwht_9.235387_Min12_Mods_Sizes.csv
• Norm_Data_Zebrafish_Top500_CV_NoOutliers_RepsAv_RowNorm.csv

Day 1 (Thursday 6/27)

• 8:30 - 9:30: RNAseq Overview (Lecture)
  • Intro and Experimental Design Slides
• 9:30 - 10:00: Post-Sequencing QC (Lecture)
  • Post Sequencing Transcriptomic Data QC Slides
• 10:00 - 10:30: Primary Processing and QC (Lecture)
  • RNA-Seq Processing Slides
• 10:30 - 10:45: BREAK
• 10:45 - 12:45: Intro to R/RStudio (Hands-on)
  • Intro to R Document
  • R_Intro.R
  • ggplot_tutorial.R
  • Tidyverse R Presentation Example
• 12:45 - 1:45: LUNCH (On your own):
• 1:45 - 2:45: Power Analysis in R & Study Design (Lecture & Hands-on)
  • Experimental Design and Power Slides
  • power_examples.R
  • Power_Example_Data.csv
• 2:45 - 3:45: RNAseq Data Analysis in R (Hands-on)
  • Analysis and Normalization Slides
  • DESeq_Workshop.R
• 3:45 - 4:00: BREAK
• 4:00 - 5:00: EMT Seminar by Mark Jankowski

Day 2 (Friday 6/28)

• 8:30 - 10:00: RNAseq Data Analysis in R (Hands-on)
  • Transcriptomic_Outlier_Finder_Workshop.R
  • Make_Colored_PCA_Plot_Workshop.R
  • makeVolcanoPlot_Workshop.R
  • Make_Heat_Map_Workshop.R
  • makeVenn_Workshop.R
• 10:00 - 10:15: BREAK
• 10:15 - 11:30: Omics Data Integration (Lecture & Hands-on)
  • BRM url: https://cbb.pnnl.gov/brm/
  • Data Integration Slides
  • BRM_BMC Bioinformatics_2019 pdf
  • File_1_Human_mRNA.txt
  • File_2_Zebrafish_mRNA.txt
  • File_3_Human_miRNA.txt
• 11:30 - 12:30: LUNCH (On your own)
• 12:30 - 2:00: Network Analysis & Visualization (Hands-on)
  • Network Analysis Slides
  • MINET_Workshop.R
  • Determine_edge_cutoff_Workshop.R
  • Filter_and_Create_Network_NEW_Workshop.R
  • Find_Modules_Workshop.R
• 2:00 - 3:00: Data Visualization with Trelliscope (Hands-on) Some general intro slides into trelliscopejs can be found here: https://slides.com/hafen/trelliscopejs/#/
  • trelliscope_intro.R
  • Zebrafish_Subset_Condition_Info.csv
  • Subset_Norm_Data_Zebrafish.csv
  • Subset_DESeq2_results.csv