├── 00_references └── SCdata_ML_slides.pdf ├── 01_singlecell_intro ├── 01_intro.Rmd ├── 01_intro.html └── media │ ├── 10x_chromium_r1_r2.png │ ├── batch_effect.png │ ├── chromium_gelbead.PNG │ ├── chromium_gem_chip.PNG │ ├── chromium_libprep.PNG │ ├── chromium_workflow.png │ ├── sc_benefits.png │ ├── sc_biol_variability.png │ └── singlecell-v.-bulk-image.png ├── 02_cellranger ├── 01_bcl_to_fastq.Rmd ├── 01_bcl_to_fastq.html ├── 02_fastq_to_bam.Rmd ├── 02_fastq_to_bam.html └── media │ ├── 10x_fastq.png │ ├── bcl2fastq_output.png │ ├── cr_count_library_csv.png │ ├── cr_count_output_files.png │ ├── gemCode_crCount_overview.png │ ├── sample_sheet.png │ ├── transcriptome_refpath.png │ └── web_summary.html ├── 03_experiment_setup ├── 01_r_setup.Rmd ├── 01_r_setup.html └── 02_data_setup.Rmd ├── 04_single_sample ├── 01_pbmc3k_sctf.Rmd ├── 01_pbmc3k_sctf.html ├── 02_pbmc3k_cluster.Rmd ├── 02_pbmc3k_cluster.html ├── 03_pbmc3k_clusterAnalysis.Rmd ├── 03_pbmc3k_clusterAnalysis.html ├── 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