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