June 13 - June 19

CSAMA10 Agenda Calendar
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Sun, Jun 13 Mon, Jun 14 Tue, Jun 15 Wed, Jun 16 Thu, Jun 17 Fri, Jun 18 Sat, Jun 19
8:30 AM 
8:30
L01: Introduction to R and Bioconductor (RG)
8:30
L05: Microarray normalisation (WH)
8:30
L09: Short read alignment (externals tools like bowtie, bwa, SSAHA, exonerate) (SA)
8:30
L13: Gene and genome annotation (PA)
8:30
L17: Chip-Seq peak finding (MM or PA)
 
   
9:00 AM   
 
9:15
L02: Overview of Bioconductor microarray analysis workflows (WH)
9:15
L06: Array quality metrics (AK)
9:15
L10: SAM/BAM (MM)
9:15
L14: RNA-Seq transcript quantification (SA)
9:15
L18: RNA-Seq, ChiP-Seq differential expression (SA)
 
   
   
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: Overview of Bioconductor packages for short read analysis (MM)
10:30
L07: Differential expression I (t-test, linear model) (RG)
10:30
L11: Differential expression II (moderation, linear model ctd, gene set enrichment) (RG)
10:30
L15: Cell-based screening (cellHTS2) (FH)
10:30
L19: Clustering and Classification with applications to microarray data and to images. Part I (GP)
 
   
11:00 AM   
 
11:15
L04: R/Bioconductor ShortRead I/O (MM)
11:15
L08: Multiple testing and independent filtering (WH)
11:15
L12: IRanges & Biostrings (PA)
11:15
L16: Cell-Assay Image Analysis (GP)
11:15
L20: Clustering and Classification with applications to microarray data and to images. Part II (GP)
 
   
   
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
 
   
   
   
2:00 PM 
2:00
Lab1: ALL dataset and Affymetrix preprocessing
2:00
Lab 3: Reading and manipulating short reads. Starting from SAM file, visualise alignments and coverage vectors, make quality-related plots. RNA-Seq: producing a feature count table
2:00
Social Program
2:00
Lab5: Differential expression
2:00
Lab7: RNA-Seq and Chip-Seq
 
   
   
   
3:00 PM   
 
3:15
Coffe break
3:15
Coffe break
3:15
Coffe break
3:15
Coffe break
 
 
3:30
Lab2: Lab1 part II
3:30
Lab4: Lab3 part II
3:30
Lab6: Lab5 part II
3:30
Lab8: Lab7 part II
 
   
4:00 PM   
   
 
4:40
Wrap up
4:40
Wrap up
4:40
Wrap up
4:40
Wrap up
 
   
5:00 PM           
           
           
           
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: Overview of Bioc...
Coffee break
L03: Overview of Bioc...
L04: R/Bioconductor S...
Pause (no lunch serve...
Installation Help Des...
Lab1: ALL dataset and...
Coffe break
Lab2: Lab1 part II
Wrap up

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