Differences

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--- mkatari-bioinformatics-august-2013 [2015/06/04 07:58] – mkatari
+++ mkatari-bioinformatics-august-2013 [2016/08/15 08:15] – mkatari
@@ Line 12: / Line 12: @@
           * 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
@@ Line 54: / Line 50: @@
   * 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://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/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://drive.google.com/file/d/0B172nc4dAaaOb0t0MWo5ZDRFY2c/view?usp=sharing|ppt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]]
+          * [[https://drive.google.com/file/d/0B172nc4dAaaOakNfZTA3OHdfbU0/view?usp=sharing|Worksheet 2]]
+          * [[https://drive.google.com/open?id=0B172nc4dAaaOZHVlYk1oODl3cE0&authuser=1|genes5expvalues]]
-  * Inferential Statistics using R
+  * Plotting using R
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOQTFjWDJJWGxLUWM/edit?usp=sharing|ppt]]
+          * [[https://drive.google.com/file/d/0B172nc4dAaaOWlh0VUlPTW5RS2c/view?usp=sharing|ppt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]]
+          * [[https://drive.google.com/file/d/0B172nc4dAaaOYXJoeTB2ZEg5Rm8/view?usp=sharing|Worksheet 3]]
           * [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]]
@@ Line 76: / Line 76: @@
   * Differential Gene Expression using DESeq
+          * [[https://drive.google.com/open?id=0B172nc4dAaaOaU82cHVNTkJ2RGM&authuser=1|RNA-seq]]
           * [[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]]
-  * 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-Phytozome2GoStats|Notes to convert Phytozome Data to GOStats]]