Manny's workshop:

• Introduction to Linux
  • Recommended software for Windows machines: MobaXterm
  • Recommended software for Apple machines: Xquartz

• Linux notes
• ppt
• Alan's information about the Cluster Using the cluster
• Alan's information about how to use SLURM Using SLURM
• More notes on shell scripts and writing SLURM batch files More Slurm
• How to use Screen Screen Notes

• Introduction to Sequence Technology
• ppt (updated Aug 22, 2014)
• Fastx toolkit
• Fastqc

• Introduction to Sequence Alignment
  • ppt
  • Blast notes
  • Bowtie notes
  • Samtools
  • MUMmer

• SNP analysis
  • Using mpileup on Samtools
  • Running samtools mpileup mpileup notes
  • Preparing files for GATK and running GATK GATK notes
  • Getting snps from a specific region VCF region

• 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