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mkatari-bioinformatics-august-2013 [2014/06/05 05:11] – mkatarimkatari-bioinformatics-august-2013 [2014/06/09 07:44] – mkatari
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           * 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]]
 +          * 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]]            * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] 
   * Introduction to Sequence Technology   * Introduction to Sequence Technology
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 Manny's R Lectures: Manny's R Lectures:
-  * R Objects and Read/Write Files -- [[https://docs.google.com/file/d/0B172nc4dAaaOZENzZGFNVEp5WTA/edit?usp=sharing|ppt]] -- [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 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]] +  * R Objects and Read/Write Files 
-  * Plotting and Writing Functions in R -- [[https://docs.google.com/file/d/0B172nc4dAaaOZ1ZoekZwcWZtT28/edit?usp=sharing|ppt]] -- [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]] +          * [[https://docs.google.com/file/d/0B172nc4dAaaOZENzZGFNVEp5WTA/edit?usp=sharing|ppt]] 
-  * Inferential Statistics using R -- [[https://docs.google.com/file/d/0B172nc4dAaaOQTFjWDJJWGxLUWM/edit?usp=sharing|ppt]] -- [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]] -- [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]] +          * [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 1]] 
-  * 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]] +          * [[https://docs.google.com/file/d/0B172nc4dAaaOTElDZkIwTUdqWU0/edit?usp=sharing|example.txt]] 
-  * Differential Gene Expression using DESeq -- [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] +          * [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]] 
-  * Clustering -- [[https://docs.google.com/file/d/0B172nc4dAaaOaC16N25EU01iXzg/edit?usp=sharing|ppt]] -- [[mkatari-bioinformatics-august-2013-clustering|Clustering]] +  * Plotting and Writing Functions in R 
-  * GeneSet Enrichment Analysis -- [[https://docs.google.com/file/d/0B172nc4dAaaOcnVlM25nWk1ZVWs/edit?usp=sharing|ppt]] -- [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]]+          * [[https://docs.google.com/file/d/0B172nc4dAaaOZ1ZoekZwcWZtT28/edit?usp=sharing|ppt]] 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]] 
 +  * Inferential Statistics using R 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaOQTFjWDJJWGxLUWM/edit?usp=sharing|ppt]] 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]] 
 +          * [[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 
 +          * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] 
 +  * Clustering 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaOaC16N25EU01iXzg/edit?usp=sharing|ppt]] 
 +          * [[mkatari-bioinformatics-august-2013-clustering|Clustering]] 
 +  * GeneSet Enrichment Analysis 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaOcnVlM25nWk1ZVWs/edit?usp=sharing|ppt]] 
 +          * [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]]
mkatari-bioinformatics-august-2013.txt · Last modified: 2017/01/25 05:13 by mkatari