Differences

This shows you the differences between two versions of the page.

--- mkatari-bioinformatics-august-2013 [2014/06/04 08:12] – mkatari
+++ mkatari-bioinformatics-august-2013 [2014/06/10 08:17] – mkatari
@@ Line 3: / Line 3: @@
 Manny's workshop:
   * Introduction to Linux
+          * Recommended software for Windows machines: [[http://mobaxterm.mobatek.net/|MobaXterm]]
+          * Recommended software for Apple machines: [[http://xquartz.macosforge.org/landing/|Xquartz]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]]
+          * 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://docs.google.com/file/d/0B172nc4dAaaOVGZIQXRWUlRmU1E/edit?usp=sharing|ppt]]
@@ Line 15: / Line 21: @@
           * [[http://samtools.sourceforge.net/samtools.shtml|Samtools]]
           * [[http://mummer.sourceforge.net/manual/|MUMmer]]
+  * SNP analysis
+          * [[https://drive.google.com/a/nyu.edu/file/d/0B172nc4dAaaOaDVMUTg5anpmMGs/edit?usp=sharing|Using mpileup on Samtools]]
   * Visualizing your alignments
           * [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]]
@@ Line 30: / Line 39: @@
 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]]