ILRI Research Computing

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====== Manny's Bioinformatics Workshop ======

Manny's workshop:
  * Introduction to Linux
          * Recommended software 
                    * Windows machines: [[http://mobaxterm.mobatek.net/|MobaXterm]]
                    * Apple machines: [[http://xquartz.macosforge.org/landing/|Xquartz]]
          * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] 
          * [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]]
          * Alan's information about the Cluster [[[[using-the-cluster|Using the cluster]]
          * Alan's information about how to use SLURM [[using-slurm|Using SLURM]]
          * More notes on shell scripts and writing SLURM batch files [[mkatari-bioinformatics-august-2013-more-slurm|More Slurm]]


  * Introduction to Sequence Technology
          * [[https://drive.google.com/file/d/0B172nc4dAaaOUGNYRFFfN1ZLOUk/edit?usp=sharing|ppt (updated Aug 22, 2014)]]
          * [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html|Fastx toolkit]]
          * [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Fastqc]]

  * Introduction to Sequence Alignment
          * [[https://docs.google.com/file/d/0B172nc4dAaaOcHlWZHM5WUw5SFE/edit?usp=sharing|ppt]]
          * [[mkatari-bioinformatics-august-2013-BlastNotes|Blast notes]]
          * [[mkatari-bioinformatics-august-2013-BowtieNotes|Bowtie notes]]
          * [[http://samtools.sourceforge.net/samtools.shtml|Samtools]]
          * [[http://mummer.sourceforge.net/manual/|MUMmer]]

  * SNP analysis
          * [[https://drive.google.com/a/nyu.edu/file/d/0B172nc4dAaaOaDVMUTg5anpmMGs/edit?usp=sharing|Using mpileup on Samtools]]
          * Running samtools mpileup [[mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup|mpileup notes]]
          * Preparing files for GATK and running GATK [[mkatari-bioinformatics-august-2013-GATKnotes|GATK notes]]
          * Getting snps from a specific region [[mkatari-bioinformatics-august-2013-VCFregion|VCF region]]

  * Visualizing your alignments
          * [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]]

  * Introduction to Mapping and Sequence Assembly
          * [[https://docs.google.com/file/d/0B172nc4dAaaOREpEdVZtSkw5dGs/edit?usp=sharing|ppt]]
          * [[http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf|Velvet Documentation]]
          * [[http://seqanswers.com/wiki/ABySS|ABySS]]

  * Introduction to RNA-seq
          * [[https://docs.google.com/file/d/0B172nc4dAaaONnVoWWJJdWlkQUU/edit?usp=sharing|ppt]]
          * [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml|Bowtie2]]
          * [[http://ccb.jhu.edu/software/tophat/manual.shtml|Tophat]]
          * [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]]
          * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]]
          * [[ http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf|DESeq manual]] 

Manny's R Lectures:

  * R Objects and Read/Write Files
          * [[https://drive.google.com/file/d/0B172nc4dAaaOU3BHbXJQYUp4ajg/view?usp=sharing|ppt]]
          * [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 1]]
          * [[https://drive.google.com/file/d/0B172nc4dAaaOcENCal94M0JMVGc/view?usp=sharing|Worksheet 1]]
          * [[https://docs.google.com/file/d/0B172nc4dAaaOTElDZkIwTUdqWU0/edit?usp=sharing|example.txt]]
          * [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]]

  * Writing Functions in R
          * [[https://docs.google.com/presentation/d/1kPLdfoDfjQokgwHuiGk1ViZ3YiBC3-A0DTVuP_EBG0A/edit?usp=sharing|ppt]]
          * [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]]         
          * [[https://drive.google.com/file/d/0B172nc4dAaaOakNfZTA3OHdfbU0/view?usp=sharing|Worksheet 2]]
          * [[https://drive.google.com/open?id=0B172nc4dAaaOZHVlYk1oODl3cE0&authuser=1|genes5expvalues]]

  * Introduction to Statistics
          * [[https://drive.google.com/file/d/0B172nc4dAaaOZlFjdW11eHFmc2s/view?usp=sharing|ppt]]

  * Plotting using R
          * [[https://drive.google.com/file/d/0B172nc4dAaaOWlh0VUlPTW5RS2c/view?usp=sharing|ppt]]
          * [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]]
          * [[https://drive.google.com/file/d/0B172nc4dAaaOYXJoeTB2ZEg5Rm8/view?usp=sharing|Worksheet 3]]
          * [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]]

  * Data cleaning and working with packages
          * [[http://www.bioconductor.org/help/workflows/high-throughput-sequencing/|Next-gen workflow]]
          * [[http://bioconductor.org|Bioconductor]]
          * [[https://docs.google.com/file/d/0B172nc4dAaaOMG44Zk1BT2NFdkU/edit?usp=sharing|Example file]]
          * [[mkatari-bioinformatics-august-2013-cleanSNP |Clean SNP data]]
          * [[mkatari-bioinformatics-august-2013-convert-SNP|Convert SNP File format]]

  * Differential Gene Expression using DESeq
          * [[https://drive.google.com/open?id=0B172nc4dAaaOaU82cHVNTkJ2RGM&authuser=1|RNA-seq]]
          * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]]

  * Clustering and GeneSet Enrichment analysis
          * [[https://drive.google.com/open?id=0B172nc4dAaaOWXRMdU1sMGlLR2M&authuser=1|ppt]]
          * [[mkatari-bioinformatics-august-2013-clustering|Clustering]]
          * [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]]
          * [[mkatari-bioinformatics-august-2013-Phytozome2GoStats|Notes to convert Phytozome Data to GOStats]]