- Introduction
- Logging In and transferring files
- Intro to command-line
- Advanced command-line
- What is Bioinformatics? (talk)
- Running jobs on the Cluster and using modules
- Files and Filetypes for RNA-Seq (talk)
- Experimental Design and Cost Estimation (talk)
- Workshop dataset talk (Emily Rustad)
- Philosophy of Preprocessing Data (talk)
- Preprocessing Data hands-on
- Intro to Sequencing, Lutz Froenicke (talk)
- Aligners (talk)
- Contamination detection
- Tag-Seq vs. RNA-Seq (talk)
- Aligning Data and IGV
- Intro to R
- Differential Gene Expression Statistics (talk)
- Alignments to Counts
- DE Analysis: counts to lists of DE genes
- Bacterial RNASeq (talk)
- Transript Assembly/Annotation (talk)
- GO/KEGG Pathway Enrichment: GO, KEGG
- Single Cell RNA-Seq (talk)
- Generating figures
- Closing thoughts
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