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mkatari-bioinformatics-august-2013 [2015/06/04 07:58] mkatarimkatari-bioinformatics-august-2013 [2017/01/25 05:13] (current) mkatari
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           * More notes on shell scripts and writing SLURM batch files [[mkatari-bioinformatics-august-2013-more-slurm|More Slurm]]           * More notes on shell scripts and writing SLURM batch files [[mkatari-bioinformatics-august-2013-more-slurm|More Slurm]]
  
-        wget ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/v5.0assembly/cassavaV5_0.chromsomesRomanNumerals.fa.gz 
- 
-[[ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/annotation/Mesculenta_147_gene.gff3.gz 
-]] 
  
   * Introduction to Sequence Technology   * Introduction to Sequence Technology
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   * R Objects and Read/Write Files   * R Objects and Read/Write Files
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOZENzZGFNVEp5WTA/edit?usp=sharing|ppt]]+          * [[https://drive.google.com/file/d/0B172nc4dAaaOU3BHbXJQYUp4ajg/view?usp=sharing|ppt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 1]]           * [[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/0B172nc4dAaaOTElDZkIwTUdqWU0/edit?usp=sharing|example.txt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]]
  
-  * Plotting and Writing Functions in R +  * Writing Functions in R 
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOZ1ZoekZwcWZtT28/edit?usp=sharing|ppt]]+          * [[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://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]]
- +          * [[https://drive.google.com/file/d/0B172nc4dAaaOYXJoeTB2ZEg5Rm8/view?usp=sharing|Worksheet 3]]
-  * 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]]           * [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]]
  
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   * Differential Gene Expression using DESeq   * Differential Gene Expression using DESeq
 +          * [[https://drive.google.com/open?id=0B172nc4dAaaOaU82cHVNTkJ2RGM&authuser=1|RNA-seq]]
           * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]]           * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]]
  
-  * Clustering +  * Clustering and GeneSet Enrichment analysis 
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOaC16N25EU01iXzg/edit?usp=sharing|ppt]]+          * [[https://drive.google.com/open?id=0B172nc4dAaaOWXRMdU1sMGlLR2M&authuser=1|ppt]]
           * [[mkatari-bioinformatics-august-2013-clustering|Clustering]]           * [[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-LoadingPhytozome|Loading Phytozome data]]
 +          * [[mkatari-bioinformatics-august-2013-Phytozome2GoStats|Notes to convert Phytozome Data to GOStats]]
mkatari-bioinformatics-august-2013.1433404683.txt.gz · Last modified: 2015/06/04 07:58 by mkatari