├── .gitignore ├── .md ├── LICENSE ├── README.md ├── Rscripts ├── cheung.R ├── cheungSubset.R ├── cltmovie.R ├── dilution.R ├── gsea.R ├── limma_quiz.R ├── make_two_tables_for_class.R ├── microarraydata-eda-lab.R └── read_tcga_meth.R ├── advinference ├── eda_for_highthroughput.Rmd ├── inference_for_highthroughput.Rmd ├── intro_to_highthroughput_data.Rmd ├── multiple_testing.Rmd ├── quick_Bioc_intro.Rmd └── storage │ ├── confounding.Rmd │ ├── crossvalidation.Rmd │ ├── distance_lecture.Rmd │ ├── heatmaps.Rmd │ ├── hierarchical_modeling.R │ ├── justsvd_duplicate_content.txt │ ├── modeling.Rmd │ ├── multtest.Rmd │ ├── pca_svd.Rmd │ ├── prediction.Rmd │ ├── sva.Rmd │ ├── svacombat.Rmd │ └── transformations.Rmd ├── batch ├── adjusting_with_factor_analysis.Rmd ├── adjusting_with_linear_models.Rmd ├── confounding.Rmd ├── eda_with_pca.Rmd ├── factor_analysis.Rmd └── intro_to_batch_effects.Rmd ├── bioc ├── EDA_plots_for_NGS.Rmd ├── HPCami.Rmd ├── aaFinalSummary.Rmd ├── anno4liftover.Rmd ├── annoCheat.Rmd ├── archWk4basic.Rmd ├── background.Rmd ├── biocparallel.Rmd ├── biological_versus_technical_var.Rmd ├── biostrings.Rmd ├── c1.all.v4.0.entrez.gmt ├── eset.Rmd ├── eset_sumexp.Rmd ├── gene_set_analysis.Rmd ├── gene_set_analysis_in_R.Rmd ├── ggbioNote.Rmd ├── grangesERBSExample.Rmd ├── importBed.Rmd ├── import_NGS.Rmd ├── inference_with_bioc.Rmd ├── installing_Bioconductor_finding_help.Rmd ├── iranges_granges.Rmd ├── moreGR.Rmd ├── normalization.Rmd ├── operateGRanges.Rmd ├── read_counting.Rmd ├── reading_microarray_data.Rmd ├── seq4motif.Rmd ├── storage │ ├── EDA_plots_for_microarray.Rmd │ ├── GEOquery.Rmd │ ├── anno1refbuilds.Rmd │ ├── anno2Biostrings.Rmd │ ├── anno3GRanges.Rmd │ ├── anno4liftover.Rmd │ ├── anno5genes.Rmd │ ├── annoPhen.Rmd │ ├── basic_Bioconductor_infrastructure.Rmd │ ├── basic_inference_microarray.Rmd │ ├── chromComp.Rmd │ ├── chromIntro.Rmd │ ├── confounding.Rmd │ ├── mapping_features.Rmd │ ├── probeSearch.Rmd │ ├── svacombat.Rmd │ ├── using_limma.Rmd │ └── using_limma_old_no_comments.Rmd ├── tophat.md ├── using_limma.Rmd └── visualizing_NGS.Rmd ├── biocadv_6x ├── bioc2_HPCami.Rmd ├── bioc2_externData.Rmd ├── bioc2_ggbio.Rmd ├── bioc2_gvfeat.Rmd ├── bioc2_hybstor.Rmd ├── bioc2_integExamps.Rmd ├── bioc2_nosql.Rmd ├── bioc2_ov.Rmd ├── bioc2_parallel.Rmd ├── bioc2_rainfall.Rmd ├── bioc2_repro1.Rmd ├── bioc2_rpacks.Rmd ├── bioc2_shiny.Rmd ├── bioc2_vizNGS.Rmd ├── bioc2_vizOv.Rmd ├── esHclust.Rmd ├── finalViz.Rmd ├── multiOOM.Rmd └── tcga.Rmd ├── biocintro_5x ├── WhatWeMeas.Rmd ├── bioc1_align.Rmd ├── bioc1_annoCheat.Rmd ├── bioc1_annoOverview.Rmd ├── bioc1_btvari.Rmd ├── bioc1_geneset_1.Rmd ├── bioc1_grangeOps.Rmd ├── bioc1_igranges.Rmd ├── bioc1_liftOver.Rmd ├── bioc1_limma.Rmd ├── bioc1_mgt_gsd.Rmd ├── bioc1_multibed.Rmd ├── bioc1_roast.Rmd ├── bioc1_summex.Rmd ├── bioc1_t_mult.Rmd ├── biointro.Rmd ├── biomotiv.Rmd ├── dataman2017.Rmd ├── dataman2019.Rmd ├── dataman2022.Rmd └── optalign.Rmd ├── chipseq ├── ChIPseq.Rmd ├── ChIPseq_quiz.R └── MACS.txt ├── eda ├── exploratory_data_analysis.Rmd └── plots_to_avoid.Rmd ├── example.Rmd ├── footnotes.R ├── highdim ├── PCA.Rmd ├── distance.Rmd ├── images │ └── handmade │ │ ├── Heatmap.png │ │ ├── SVD1.png │ │ ├── SVD2.png │ │ └── animals.png ├── mds.Rmd ├── pca_motivation.Rmd ├── projections.Rmd ├── rotations.Rmd └── svd.Rmd ├── inference ├── R_refresher.Rmd ├── association_tests.Rmd ├── clt_and_t-distribution.Rmd ├── clt_in_practice.Rmd ├── confidence_intervals.Rmd ├── monte_carlo.Rmd ├── permutation_tests.Rmd ├── populations_and_samples.Rmd ├── power_calculations.Rmd ├── random_variables.Rmd └── t-tests_in_practice.Rmd ├── intro ├── dplyr_intro.Rmd ├── dplyr_tutorial.Rmd ├── getting_started.Rmd ├── github.Rmd ├── introduction.Rmd ├── math_notation.Rmd └── system_files.Rmd ├── linear ├── collinearity.Rmd ├── expressing_design_formula.Rmd ├── interactions_and_contrasts.Rmd ├── linear_models_going_further.Rmd ├── linear_models_in_practice.Rmd ├── linear_models_intro.Rmd ├── qr_and_regression.Rmd └── standard_errors.Rmd ├── list_libs.sh ├── makefile ├── matrixalg ├── intro_using_regression.Rmd ├── matrix_algebra_examples.Rmd ├── matrix_notation.Rmd └── matrix_operations.Rmd ├── methyl ├── epiviz.Rmd ├── inference_for_DNAmeth.Rmd ├── methylation.Rmd └── minfi.Rmd ├── ml ├── clustering_and_heatmaps.Rmd ├── conditional_expectation.Rmd ├── crossvalidation.Rmd ├── machine_learning.Rmd └── smoothing.Rmd ├── modeling ├── bayes-gif.R ├── bayes.Rmd ├── hierarchical_models.Rmd └── modeling.Rmd ├── renaming_map.md ├── rnaseq ├── airway_sample_table.csv ├── fastq.md ├── genome_align_STAR.md ├── r_bioc_links.md ├── rnaseq_exon_usage.Rmd ├── rnaseq_gene_level.Rmd ├── rnaseq_isoform_cummerbund.Rmd ├── rnaseq_pkgs.R ├── storage │ ├── RNAseq_quiz.R │ └── cufflinks.txt └── trancsript_align_RSEM.md ├── robust ├── ranktest.Rmd └── robust_summaries.Rmd └── variants ├── SNP.Rmd └── SNP_quiz.R /.gitignore: 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