Manny's workshop:

• Introduction to Linux – ppt – Linux notes
• Introduction to Sequence Technology – ppt – Fastx toolkit – Fastqc
• Introduction to Sequence Alignment – ppt – Blast notes – Bowtie notes – Samtools
• * MUMmer
• Visualizing your alignments – IGVnotes
• Introduction to Mapping and Sequence Assembly – ppt – Velvet Documentation – ABySS
• Introduction to RNA-seq – ppt – Bowtie2 – Tophat – Cufflinks – CuffDiff – DESeq manual

Manny's R Lectures:

• R Objects and Read/Write Files – ppt – Exercise 1 – example.txt – example.csv
• Plotting and Writing Functions in R – ppt – breast cancer dataset
• Inferential Statistics using R – ppt – Normalized Data – Volcano plot
• Data cleaning and working with packages – Next-gen workflow – Bioconductor – Example file – – Clean SNP data – – Convert SNP File format
• Differential Gene Expression using DESeq – DESeq
• Clustering – ppt – Clustering
• GeneSet Enrichment Analysis – ppt – Loading Phytozome data