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vjcitn committed Sep 16, 2013
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Complexity, poor design, batch effects. Vehicles for
avoiding some of the pitfalls with Bioconductor.

* Lab 1: Managing genomic annotation for humand and model organisms
+ OrganismDbi, select
+ GenomicRanges
* Lab 1: Managing genomic annotation for human and model organisms
+ _OrganismDbi_, _select_
+ _GenomicRanges_

* Lab 2: Managing and using experimental archives
+ General principle: X[G, S] is selection of genomic features G
and experimental samples S from archive X
+ Archive containers: ExpressionSet, SummarizedExperiment
+ General principle: `X[G, S]` is selection of genomic features `G`
and experimental samples `S` from archive `X`
+ Archive containers: `ExpressionSet`, `SummarizedExperiment`
+ Getting acquainted with some classic experiments
- Expression arrays
- Methylation arrays
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* Lab 4: Case studies
+ Microarray differential expression
+ Differential methylation
+ RNA-seq, DESeq
+ ChIP-seq, bsseq, DiffBind
+ RNA-seq, _DESeq_
+ ChIP-seq, _bsseq_, _DiffBind_
+ Integrative analyses

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