mkatari-bioinformatics-august-2013
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- | * [[mkatari-bioinformatics-august-2013-day1]] | + | |
+ | * Recommended software | ||
+ | * Windows machines: [[http:// | ||
+ | * Apple machines: [[http:// | ||
+ | * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] | ||
+ | * [[https:// | ||
+ | * 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:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | |||
+ | * Introduction to Sequence Alignment | ||
+ | * [[https:// | ||
+ | * [[mkatari-bioinformatics-august-2013-BlastNotes|Blast notes]] | ||
+ | * [[mkatari-bioinformatics-august-2013-BowtieNotes|Bowtie notes]] | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | |||
+ | * SNP analysis | ||
+ | * [[https:// | ||
+ | * 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:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | |||
+ | * Introduction to RNA-seq | ||
+ | * [[https:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[ http:// | ||
+ | |||
+ | Manny' | ||
+ | |||
+ | * R Objects and Read/Write Files | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | |||
+ | * Writing Functions in R | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | |||
+ | * Plotting using R | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]] | ||
+ | |||
+ | * Data cleaning and working with packages | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[https:// | ||
+ | * [[mkatari-bioinformatics-august-2013-cleanSNP |Clean SNP data]] | ||
+ | * [[mkatari-bioinformatics-august-2013-convert-SNP|Convert SNP File format]] | ||
+ | |||
+ | * Differential Gene Expression using DESeq | ||
+ | * [[https:// | ||
+ | * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] | ||
+ | |||
+ | * Clustering and GeneSet Enrichment analysis | ||
+ | * [[https:// | ||
+ | * [[mkatari-bioinformatics-august-2013-clustering|Clustering]] | ||
+ | * [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]] | ||
+ | |
mkatari-bioinformatics-august-2013.txt · Last modified: 2017/01/25 05:13 by mkatari