├── .gitignore ├── LICENSE ├── README.md ├── bioc ├── GRL.Rmd ├── anno.qmd ├── bioc_anno_strings_HW.Rmd ├── bioc_objects_ranges_HW.Rmd ├── chr1_100Mb_v86_txps.bed ├── chr1_query.bed ├── make_ranges_and_BED.R ├── my_scale_counts.R ├── objects.qmd ├── promoter_CpG.R ├── ranges.qmd └── strings.qmd ├── dist ├── batch.qmd ├── dist_biases_scaling_HW.Rmd ├── distances.qmd ├── geuvadis.tsv ├── ruv.R ├── sva.qmd ├── transform_clust.qmd └── vst_math.qmd ├── eda ├── EDA.qmd ├── NAs.Rmd ├── brain_RNA.qmd ├── functions.md ├── organisms.tsv ├── organisms_genes.tsv └── scrape_ensembl.R ├── github └── github_HW.Rmd ├── hier ├── hierarchical.Rmd ├── hierarchical_iterate.R ├── jamesstein.Rmd ├── simple.stan ├── simple_hierarchical.R └── simple_stan.R ├── markov └── hmm.Rmd ├── model ├── EM.Rmd ├── model_HW.Rmd ├── motif.Rmd ├── motif_scratch.Rmd └── yy1_seqs.csv.gz ├── multiple ├── IDR.Rmd ├── localfdr.Rmd └── multtest.Rmd └── net └── network.Rmd /.gitignore: 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