- R, RStudio, and Bioconductor
- Terminal, git, and GitHub
- Cluster setup - specific to Longleaf cluster at UNC
- Snakemake
- downloading files from European Nucleotide Archive
- quantify transcripts with RNA-seq
- g2gtools or EMASE on cluster
- aligning sequencing reads to genome
- ReportingTools to build a differential expression analysis report
- FASTQC and MultiQC for quality control of sequence data
- IGV for exploring genomic files