├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── README.md ├── data ├── qa_all.rda └── stats0.rda ├── inst ├── doc │ └── hg19_alias.tab ├── extdata │ ├── ALLphenoData.tsv │ ├── NCI60.Rda │ ├── nci.data │ └── nci.info └── script │ └── creatingNCI60.R └── vignettes ├── A01.1_IntroductionToR.Rmd ├── A01.2_IntroductionToBioconductor.Rmd ├── A01.3_BioconductorForSequenceAnalysis.Rmd ├── A01_Introduction.Rmd ├── B02.1.1_RNASeqLab.Rmd ├── B02.1_RNASeq.Rmd ├── B02.2.3_CopyNumber.Rmd ├── B02.2_CommonWorkFlows.Rmd ├── B02.3_MachineLearning.Rmd ├── B02.4_Annotation.Rmd ├── B02.5_GeneSetEnrichment.Rmd ├── C03.1_LargeData.Rmd ├── C03.2_CodeToPackages.Rmd ├── C03.3_ReproducibleResearch.Rmd ├── C03.4_Visualization.Rmd ├── D04.1_InstallIGV.Rmd ├── hg19_alias.tab └── our_figures ├── GRanges.png ├── GRangesList.png ├── RangeOperations.png ├── SequencingEcosystem.png ├── SequencingEcosystem_no_bioc_pkgs.png ├── Solexa-bridge-pcr.jpg ├── SummarizedExperiment.png ├── copy_number_QC_2.png ├── 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