Topics in development

[rkhetani]

• 1. Salmon/sleuth (Prereq: familiarity with HPC, bash and R)

• 2. SRA/GEO data download (Prereq: familiarity with HPC and bash)

• 3. Sequence data QC (fastqc, multiqc, qualimap) (Prereq: familiarity with HPC and bash)

• 4. IGV for publication worthy figures

• 5. Advanced bash (awk/sed) (Prereq: familiarity with HPC and bash) #24

• 6. Gene Annotation in R (ensembldb, annotationhub etc.) (Prereq: familiarity with R)

• 7. Version Control with Git (Prereq: familiarity with HPC and bash)

• 8. Version Control with Git using GitKraken

• 9. Differential Gene Expression (DGE) analysis with DESeq2 (Prereq: familiarity with R)

• 10. Introduction to Python

• 11. Sample group clustering with heatmaps and PCA (Principal Component Analysis) (Prereq: familiarity with R)

• 12. Exploring genome variation using the GEMINI framework (Prereq: familiarity with HPC and bash)

• 13. Introduction to tidyverse R packages for data visualization (Prereq: familiarity with R)

• 14. Intro to shell

[marypipes]

• 15. Functions and automation in R: creating functions, purrr:map family of functions, apply family? , practice with writing functions and apply across a list, data frame, elements in a vector, etc., creating a function to read in multiple files of gene lists and creating heat maps for each?, reading in multiple gmt files to do GSEA analysis on all?

• 16. Creating R package (as own or with previous): how to combine custom functions into a package that you can load for every analysis, if Mike wants to help, then we could talk about creating a package to share on bioconductor or CRAN and important considerations.

[marypiper]

• 17. Visualization and functional analysis of genomic coordinates from NGS analyses (peak calls, etc.)