June 23 - June 29

CSAMA 2013 Agenda Calendar
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Sun, Jun 23 Mon, Jun 24 Tue, Jun 25 Wed, Jun 26 Thu, Jun 27 Fri, Jun 28 Sat, Jun 29
8:30 AM 
8:30
L01: Introduction to R and Bioconductor (MM)
8:30
L05: Visualisation (VJC)
8:30
L09: Elements of statistics 2: Classification and regularisation (1h WH)
8:30
L13: Leveraging annotation and data integration: working with gene and genome annotations (MM)
8:30
L13: Gene set enrichment analysis (RG)
 
   
9:00 AM   
 
9:15
L02: Basics of high-throughput sequencing technologies and short read aligners (SA)
9:15
L06: RNA-Seq 1: differential expression analysis and error models (SA)
9:15
L14: eQTL / molecular-QTL analyses; integrative analysis of the Cancer Cell Line Encyclopedia (VJC)
9:15
L14: DNA Variant Calling (RG)
 
 
9:30
L10: DNA-methylation; selected topics in epigenetics and ChIP-Seq (2h; MR)
 
   
10:00 AM 
10:00
Coffee break
10:00
Coffee break
10:00
Coffee break
10:00
Coffee break
10:00
Coffee break
 
   
 
10:30
L03: Elements of statistics 1: t-test and linear model (RG)
10:30
L07: RNA-Seq 2: NB-GLMs, and application to alternative exon usage (SA)
10:30
L11: DNA-methylation; selected topics in epigenetics and ChIP-Seq (2h; MR)
10:30
L15: Elements of statistics 3: multiple testing and independent filtering (WH)
10:30
L15: Hilbert curve (SA) + Motifs, PWMs (MM)
 
   
11:00 AM   
 
11:15
L04: What you still may want to know about microarrays (WH)
11:15
L08: Computing with genomic ranges, sequences and alignments (MM)
11:15
L12: DNA-methylation; selected topics in epigenetics and ChIP-Seq (2h; MR)
11:15
L16: Emerging topic (TBC)
11:15
L16: Emerging topic (TBC)
 
   
   
12:00 PM 
12:00
Pause (no lunch served)
12:00
Pause (no lunch served)
12:00
Pause (no lunch served)
12:00
Pause (no lunch served)
12:00
Pause (no lunch served)
 
   
   
   
1:00 PM 
1:00
Installation Help Desk (2)
 
   
   
   
2:00 PM 
2:00
Tutorial1: R Intro, Part1. Note: Students taking the Advanced R Tutorial on friday, will instead do Lab 3 during this time.
2:00
Lab 1: Complete RNA-Seq workflow (from FASTQ to GSEA). Part 1
2:00
Social Program
2:00
Lab2: DNA-Seq analysis: from a human genome (subset of Illumina shotgun WGS) to annotated variants. Part 1
2:00
Tutorial2: Advanced topics in R - functional programming, parallelization, S4, debugging, writing packages
2:00
Lab3: Annotation and visualization. Part 1
 
   
   
   
3:00 PM   
 
3:15
Coffe break
3:15
Coffe break
3:15
Coffe break
3:15
Coffe break
 
 
3:30
Tutorial1: part II o Lab3 part II
3:30
Lab1: Part 2
3:30
Lab2: RDNA-Seq analysis: from a human genome (subset of Illumina shotgun WGS) to annotated variants. Part 2
3:30
Lab3: Part 2
3:30
Tutorial2: Part 2
 
   
4:00 PM   
   
 
4:40
Wrap up
4:40
Wrap up
4:40
Wrap up
4:40
Wrap up
 
   
5:00 PM
5:00
Installation Help Desk (1)
5:00
Flashlight Session 1
5:00
Flashlight Session 2
5:00
Flashlight Session 3
   
   
         
         
6:00 PM
6:00
Meet Together
         
         
         
         
7:00 PM         
         
         
         
8:00 PM         
         
           
           
9:00 PM           
           
           
           
10:00 PM             
             
             
             
11:00 PM             
             
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L01: Introduction to ...
L02: Basics of high-t...
Coffee break
L03: Elements of stat...
L04: What you still m...
Pause (no lunch serve...
Installation Help Des...
Tutorial1: R Intro, P...
Coffe break
Tutorial1: part II o ...
Wrap up
Flashlight Session 1

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