June 26 - July 2

CSAMA 2011 Agenda Calendar
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Sun, Jun 26 Mon, Jun 27 Tue, Jun 28 Wed, Jun 29 Thu, Jun 30 Fri, Jul 1 Sat, Jul 2
8:30 AM 
8:30
L01: Introduction to R and Bioconductor (RG)
8:30
L05: Short read alignment using externals tools like bowtie, bwa, SOAP (KDH)
8:30
L09: t-test and linear model - the general statistical concepts (RG)
8:30
L13: Methods for visualising your data along genomic coordinates - Rtracklayer (VJC), IGB (RG), GenomeGraphs (KDH)
8:30
L17: Machine Learning - Clustering and Classification (VJC)
 
   
9:00 AM   
 
9:15
L02: Bioconductor packages for sequence analysis (MM)
9:15
L06: Working with sequences: exploratory analysis, quality assessment, and remeidation -- Biostrings, ShortRead, Rsamtools (MM)
9:15
L10: RNA-Seq differential expression (WH)
9:15
L14: ChIP-Seq related topics (RG)
9:15
L18: Aggregation - gene set enrichment analysis (RG)
 
   
   
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: Reproducible workflows with R (VJC)
10:30
L07: IRanges, GenomicRanges (KDH)
10:30
L11: Multiple testing and independent filtering (WH)
10:30
L15: eQTL-type analyses (VJC)
10:30
L19: Automated image analysis for high content screening; genetic interactions (WH)
 
   
11:00 AM   
 
11:15
L04: Basics of HT sequencing technologies (KDH)
11:15
L08: What one still might want to know about microarray data: normalisation, QA/QC (WH)
11:15
L12: Annotating Genes and Genomic Ranges - GenomicFeatures; AnnotationDbi; org* (MM)
11:15
L16: Emerging topic
11:15
L20: Whole genome bisulfite sequencing - DNA methylation (KDH)
 
   
   
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
Lab1: Two options, for R 'beginners' and 'experts': Tutorial (lecture + practical exercises): Basics of R - data types, control, functions, reading and writing text files and spreadsheet tables (AK) XOR Machine Learning (VJC)
2:00
Lab 3: Reading and manipulating short reads (MM) Starting BAM files, assess quality, visualise alignments and coverage vectors, produce a feature count table.
2:00
Social Program
2:00
Lab5: Statistical methods for differential expression - DESeq; Differential analysis of exon usage - DEXSeq (WH)
2:00
Lab7: ggtut: integrative analysis, GGE / GSEA, e.g. use microarray expression and genotype, do eQTL, and a GSEA (VJC) A ChIP-Seq application - HiC (WH) ML - for those who didn't do it on Monday
 
   
   
   
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
5:00
Installation Help Desk (1)
         
         
         
         
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 ...
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Coffee break
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Installation Help Des...
Lab1: Two options, fo...
Coffe break
Lab2: Lab1 part II
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