mkatari-bioinformatics-august-2013
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mkatari-bioinformatics-august-2013 [2013/08/13 14:21] – mkatari | mkatari-bioinformatics-august-2013 [2015/05/21 13:38] – mkatari | ||
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- | ====== Manny' | + | ====== Manny' |
Manny' | Manny' | ||
- | * Introduction to Linux -- [[https:// | + | * Introduction to Linux |
- | * Introduction to Sequence Technology | + | * Recommended software for Windows machines: [[http:// |
- | * Introduction to Sequence Alignment | + | * Recommended software for Apple machines: [[http:// |
- | * Introduction to Mapping and Sequence Assembly -- [[https:// | + | * [[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]] | ||
+ | * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] | ||
+ | * How to use Screen [[mkatari-bioinformatcs-august-2013-ScreenNotes|Screen Notes]] | ||
+ | | ||
+ | * Introduction to Sequence Technology | ||
+ | * [[https://drive.google.com/ | ||
+ | * [[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:// | ||
+ | |||
+ | * Plotting and Writing Functions in R | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | |||
+ | * Inferential Statistics using R | ||
+ | * [[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 | ||
+ | * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] | ||
+ | |||
+ | * Clustering | ||
+ | * [[https:// | ||
+ | * [[mkatari-bioinformatics-august-2013-clustering|Clustering]] | ||
+ | |||
+ | * GeneSet Enrichment Analysis | ||
+ | * [[https:// | ||
+ | * [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]] |
mkatari-bioinformatics-august-2013.txt · Last modified: 2017/01/25 05:13 by mkatari