mkatari-bioinformatics-august-2013
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
mkatari-bioinformatics-august-2013 [2014/06/05 05:11] – mkatari | mkatari-bioinformatics-august-2013 [2015/08/24 05:38] – mkatari | ||
---|---|---|---|
Line 3: | Line 3: | ||
Manny' | Manny' | ||
* Introduction to Linux | * Introduction to Linux | ||
- | * Recommended software | + | * Recommended software |
- | * Recommended software for Apple machines: [[http:// | + | * Windows machines: [[http:// |
+ | * Apple machines: [[http:// | ||
+ | * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] | ||
* [[https:// | * [[https:// | ||
* Alan's information about the Cluster [[[[using-the-cluster|Using the cluster]] | * Alan's information about the Cluster [[[[using-the-cluster|Using the cluster]] | ||
* Alan's information about how to use SLURM [[using-slurm|Using SLURM]] | * Alan's information about how to use SLURM [[using-slurm|Using SLURM]] | ||
- | * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] | + | * More notes on shell scripts and writing SLURM batch files [[mkatari-bioinformatics-august-2013-more-slurm|More Slurm]] |
+ | |||
* Introduction to Sequence Technology | * Introduction to Sequence Technology | ||
- | * [[https://docs.google.com/ | + | * [[https://drive.google.com/ |
* [[http:// | * [[http:// | ||
* [[http:// | * [[http:// | ||
+ | |||
* Introduction to Sequence Alignment | * Introduction to Sequence Alignment | ||
* [[https:// | * [[https:// | ||
Line 19: | Line 24: | ||
* [[http:// | * [[http:// | ||
* [[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 | * Visualizing your alignments | ||
* [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]] | * [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]] | ||
+ | |||
* Introduction to Mapping and Sequence Assembly | * Introduction to Mapping and Sequence Assembly | ||
* [[https:// | * [[https:// | ||
* [[http:// | * [[http:// | ||
* [[http:// | * [[http:// | ||
+ | |||
* Introduction to RNA-seq | * Introduction to RNA-seq | ||
* [[https:// | * [[https:// | ||
* [[http:// | * [[http:// | ||
- | * [[http://tophat.cbcb.umd.edu/ | + | * [[http://ccb.jhu.edu/ |
* [[http:// | * [[http:// | ||
* [[http:// | * [[http:// | ||
Line 34: | Line 48: | ||
Manny' | Manny' | ||
- | | + | |
- | * Plotting and Writing Functions in R -- [[https://docs.google.com/ | + | |
- | * Inferential Statistics | + | * [[https://drive.google.com/ |
- | * Data cleaning and working with packages | + | * [[https:// |
- | * Differential Gene Expression using DESeq -- [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] | + | * [[https:// |
- | * Clustering -- [[https://docs.google.com/ | + | * [[https:// |
- | * GeneSet Enrichment | + | * [[https:// |
+ | |||
+ | * Writing Functions in R | ||
+ | * [[https://drive.google.com/ | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | |||
+ | * Plotting | ||
+ | * [[https://drive.google.com/ | ||
+ | * [[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://drive.google.com/ | ||
+ | * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] | ||
+ | |||
+ | * Clustering and GeneSet Enrichment | ||
+ | * [[https://drive.google.com/ | ||
+ | * [[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