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means done

week 1

  • mike RStudio

  • mike R refresher

  • mike Installing Bioconductor and finding help

  • rafa Exploratory data analysis

week 2

  • mike github

  • rafa Reading microarray raw data

  • rafa Microarray EDA

  • mike Mapping algorithms and software

  • mike NGS EDA

  • mike Basic Bioconductor infrastructure: IRanges

  • mike Basic Bioconductor infrastructure: GenomicRanges

  • mike Basic Bioconductor infrastructure: ExpressionSet and SummarizedExperiment

week 3

  • rafa Monte carlo simulation

  • rafa Permutation tests

  • mike Expressing experimental design using R formula

  • mike Basic inference on microarray part I

  • mike Basic inference on microarray part II

week 4

  • rafa Motivating normalization with EDA

  • rafa Normalizing microarrays

week 5

  • mike Distances, clustering

  • mike MDS, heatmaps

  • mike cross-validation

week 6

  • rafa Combat, SVA in R

  • mike PCA and SVD in R

  • TODO: show how to get date from the celfiles.

week 7

  • mike Using the limma package

  • mike Mapping features to genes

  • mike Gene set testing

week 8

  • mike Visualizing NGS with Bioconductor, IGV

  • mike Making NGS read count table in Bioconductor

  • mike SNVs

  • mike RNA-seq

  • rafa DNA methylation: arrays and NGS

  • mike ChIP-seq