├── CITE-seq.md ├── DimReds.md ├── ExpHub_submission.md ├── GOterm_overrepresentation.md ├── IntroToNGS_WCMGS.md ├── README.md ├── RNA_heteroskedasticity.Rmd ├── RNA_heteroskedasticity.md ├── RNA_heteroskedasticity_files └── figure-html │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-5-1.png │ ├── unnamed-chunk-8-1.png │ └── unnamed-chunk-9-1.png ├── Seurat.md ├── Seurat_labelTransfer.md ├── alignment_vs_pseudoalignment.md ├── atac.md ├── bashrc ├── clusterProfiler_with_goseq.md ├── dna_methylation.md ├── gene_set_enrichment_analyses.md ├── hidden_markov_model.md ├── images ├── GSEA.png ├── GSEA02.png ├── GSEA_Barbie.png ├── GSEA_Verhaak.png ├── GSEA_ssGSEA.png ├── HMM_01.png ├── MA_GCprobes.png ├── MA_NUSE.png ├── MA_PLM.png ├── MA_RLE.png ├── MA_differentProbesets.png ├── MA_mapping.png ├── MA_medianPolish.png ├── MA_normMethodComparison_TACmanual.png ├── MA_oneColor.png ├── MA_rma.png ├── MA_twoColors.png ├── MA_types.png ├── intro │ ├── AuerDoerge2010.png │ ├── biology-02-00378-g001.jpg │ ├── ngsapps.png │ ├── replicates.png │ ├── replicates2.png │ └── wcm_schema.png ├── nanopore_principle.png ├── nanopore_processing.png ├── nanopore_processing02.png └── tcgsa │ ├── baselineD1.png │ ├── clst3.png │ ├── clust2.png │ ├── hm_baseline.png │ ├── noBaseline.png │ └── noBaseline_precluster.png ├── integrativeAnalysis.md ├── karyotype.md ├── metabolomics.md ├── microarrays.md ├── motif_analyses.md ├── nanopore_sequencing.md ├── notes_10Q.md ├── proteomics.md ├── references └── GSEA │ ├── lec14a.pdf │ └── ssGSEA_caw_BIG_120314.pptx ├── repeatMasker.md ├── repetitiveElements.md ├── revigo.md ├── rscript.md ├── scRNA-seq.md ├── scRNA-seq_RNAvelocity.md ├── scRNA-seq_python ├── installing_scanpyEtc.sh └── scRNA-seq_scanorama.Rmd ├── scRNA-seq_zinbwave_zinger.R ├── scRRBS.md ├── shiny.md ├── spatial_transcriptomics.md └── vdj_tcr_sequencing.md /CITE-seq.md: 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