├── README.md ├── archive └── cut_and_paste.txt ├── cegs_2016.Rpres ├── cegs_2017.html ├── cegs_2017.md ├── docker └── Dockerfile ├── images ├── 10X_gem.png ├── 10X_paper.png ├── 10X_wet.png ├── 10X_wet_mol.png ├── 10x_rnaseq.png ├── 10x_web.png ├── Drop-seq-chip-large.jpg ├── PCA_plot_02.gif ├── Rstudio_overview.png ├── aligncount.png ├── batch_effects_2.png ├── batch_effects_3.pdf-g3380-229.png ├── batch_effects_3.png ├── batch_effects_4.png ├── cell_cycle.png ├── cell_cycle_1.png ├── cell_cycle_collapse.png ├── clpca.png ├── compare_assays.png ├── compare_power_paper.png ├── compare_umi.png ├── complex_tissues.png ├── confounding.png ├── confounding_paper.png ├── corgis │ ├── corgi_can.jpg │ ├── corgi_clump.jpg │ ├── corgi_saturation.jpg │ ├── dogbutt.jpg │ ├── driving_corgi.jpg │ ├── fall.jpg │ ├── fancy.jpg │ ├── graduate_corgi.jpg │ ├── ninja_corgi.jpeg │ ├── outlier_corgi.jpg │ ├── pillows.jpg │ ├── professor_corgi.jpg │ ├── puppies.jpg │ ├── scientist.jpg │ ├── tea.jpg │ └── tie_corgi.jpeg ├── drop_seq_equipment.jpeg ├── drop_seq_web.png ├── dropseq_1.jpg ├── dropseq_2.png ├── dropseq_assay_1.png ├── dropseq_assay_umi.png ├── dropseq_drops.gif ├── dropseq_equipment.png ├── dropseq_fluidics.png ├── dropseq_fluidics_big.png ├── dropseq_paper.png ├── dropseq_rnaseq.png ├── dropseq_seperating_cells.png ├── fastq.png ├── hold │ ├── cell_cycle.pdf │ └── mclust.pdf ├── itay_paper.png ├── karthik_retina_paper.png ├── nextseq-large.jpg ├── pagoda_methodology.png ├── pagoda_paper.png ├── plate.jpg ├── population_rnaseq.png ├── population_rnaseq_qc.png ├── prevalence.png ├── prob_ave_expression.png ├── prob_ave_expression2.png ├── prob_ave_expression3.png ├── raceid_pubs.png ├── reads.png ├── rna_seq_summary.png ├── sc_sequences.png ├── scater_paper.png ├── scde_bio.png ├── scde_intro.png ├── scde_output.png ├── scde_output_2.png ├── scdistributions_all.png ├── scdistributions_bimodal.png ├── scdistributions_log_normal.png ├── scdistributions_noise.png ├── scdistributions_zeroinfl.png ├── sequencing-methods-review.png ├── seurat_pubs.pdf-g14-630.png ├── seurat_pubs.png ├── shekhar_cell_type.png ├── single_cell_clinical.png ├── smart_seq2.jpg ├── smart_seq2.png ├── smartseq_paper.png ├── smartseq_protocols.png ├── sparseMatrices.png ├── starting_matrix.png ├── top_pwca.png ├── tsne.png ├── umi.png └── varinfo.png └── install.Rhistory /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TimothyTickle/single_cell_analysis/HEAD/README.md -------------------------------------------------------------------------------- /archive/cut_and_paste.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TimothyTickle/single_cell_analysis/HEAD/archive/cut_and_paste.txt -------------------------------------------------------------------------------- /cegs_2016.Rpres: 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