├── EB_cells ├── QC │ ├── .DS_Store │ └── QC_accmet.Rmd ├── README.md ├── acc_conservation │ ├── .DS_Store │ ├── .Rhistory │ ├── accrna_cluster.Rmd │ ├── accrna_lik_ratio.Rmd │ ├── plot_gene_examples.Rmd │ ├── plot_sc_profiles.Rmd │ └── scripts │ │ ├── .DS_Store │ │ ├── .Rhistory │ │ ├── cluster_lineage_profiles_400bp.R │ │ ├── cluster_profiles_200bp.R │ │ ├── cluster_profiles_400bp.R │ │ ├── learn_profiles_1k.R │ │ ├── learn_profiles_200bp.R │ │ └── learn_profiles_400bp.R ├── correlations │ ├── .DS_Store │ ├── .Rhistory │ ├── accrna.Rmd │ ├── metacc.Rmd │ ├── metrna.Rmd │ └── utils.R ├── differential │ ├── .DS_Store │ ├── .Rhistory │ └── differential_expr.Rmd ├── dimensionality_reduction │ ├── .DS_Store │ ├── ZIFA.Rmd │ ├── expr_dimensionality_reduction.Rmd │ └── met_dimensionality_reduction.Rmd ├── heatmap │ ├── .DS_Store │ ├── .Rhistory │ ├── heatmap_acc.Rmd │ ├── heatmap_met.Rmd │ └── heatmap_rna.Rmd ├── preprocessing │ ├── .DS_Store │ ├── metacc │ │ ├── README.txt │ │ ├── annotate.R │ │ ├── assign_strand.R │ │ ├── binarise.R │ │ ├── merge.R │ │ ├── merge_sites.R │ │ ├── pseudobulk_metacc.R │ │ ├── raw_filter.R │ │ └── raw_filter.sh │ └── rna │ │ └── preproc_rna.Rmd ├── pseudobulk_profiles │ ├── .DS_Store │ ├── .Rhistory │ └── metacc_profiles.Rmd ├── pseudotime │ ├── .DS_Store │ ├── .Rhistory │ ├── coupling.Rmd │ ├── destiny.Rmd │ ├── pseudotime_profiles │ │ ├── .DS_Store │ │ ├── .Rhistory │ │ ├── .ipynb_checkpoints │ │ │ └── Untitled-checkpoint.ipynb │ │ ├── lineage_clusters.Rmd │ │ ├── plot_lineage_clusters.Rmd │ │ ├── plot_lineage_clusters_metacc.Rmd │ │ ├── pseudotime_cluster.Rmd │ │ └── scripts │ │ │ ├── .Rhistory │ │ │ ├── cl_cellwise_par.R │ │ │ ├── cl_cellwise_par_all_BIC.R │ │ │ ├── cl_cellwise_par_same_genes.R │ │ │ ├── cluster_lineage_profiles_400bp.R │ │ │ ├── cluster_lineage_profiles_cell_wise.R │ │ │ ├── learn_profiles_400bp cell_wise.R │ │ │ └── learn_profiles_400bp.R │ └── utils.R ├── stats │ ├── .DS_Store │ ├── .Rhistory │ ├── stats_accmet_features_parsed.Rmd │ └── stats_accmet_samples_raw.Rmd └── zoom │ ├── .DS_Store │ ├── .Rhistory │ ├── zoom_annotation.R │ └── zoom_lineage.R ├── README.md ├── protocol.png └── serum_cells ├── QC ├── .DS_Store ├── metacc │ ├── .DS_Store │ ├── .Rhistory │ ├── QC_accmet.Rmd │ └── bismark_report.txt └── rna │ ├── .Rhistory │ └── QC_expr.Rmd ├── README.md ├── Rutils ├── .DS_Store ├── Met_functions.R ├── RNA_functions.R ├── plot_functions.R ├── preproc_dna.R ├── preprocess_functions.R └── stats_utils.R ├── bulk_comparison ├── .DS_Store ├── acc │ ├── comparison_scNMT.R │ ├── preproc_acc.R │ └── test.R ├── accrna │ ├── .DS_Store │ ├── .Rhistory │ └── cor_accrna.R ├── met │ ├── annotate_met.R │ ├── cor_replicates_met.R │ ├── parse_met.R │ └── preproc_met.R ├── metacc │ ├── cor_metacc.R │ └── out │ │ └── cor_metacc.txt └── metrna │ ├── cor_metrna.R │ └── out │ └── cor_metrna.txt ├── correlations ├── .DS_Store ├── .Rhistory ├── accrna │ ├── .DS_Store │ ├── .Rhistory │ └── accrna.Rmd ├── local_accrna │ ├── .DS_Store │ ├── .Rhistory │ ├── TSS.bed.gz │ ├── cor_local_dnarna.Rmd │ └── run.R ├── metacc │ ├── .DS_Store │ ├── .Rhistory │ └── metacc.Rmd ├── metrna │ ├── .DS_Store │ └── metrna.Rmd └── utils.R ├── dimensionality_reduction ├── .DS_Store ├── .Rhistory ├── ZIFA.Rmd ├── acc_dimreduction.Rmd ├── met_dimreduction.Rmd ├── out │ ├── ZIFA_out.pdf │ ├── ZIFA_out_12.pdf │ ├── ZIFA_out_23.pdf │ ├── expr.csv │ └── output.ZIFA.txt └── rna_dimreduction.Rmd ├── genesets ├── differentiation.tsv ├── housekeeping.tsv ├── pluripotency.tsv └── pluripotency_extended.tsv ├── heatmap ├── .DS_Store ├── .Rhistory ├── heatmap_acc.Rmd ├── heatmap_met.Rmd ├── heatmap_rna.Rmd └── heatmap_rna_previousdatasets.Rmd ├── method_performance ├── DHS_comparision.Rmd ├── DNase_promoters.Rmd ├── load_pub_data.Rmd ├── met_comparison.Rmd └── qc_coverage.Rmd ├── preprocessing ├── .DS_Store ├── .Rhistory ├── .Rproj.user │ └── 89808701 │ │ ├── pcs │ │ ├── files-pane.pper │ │ ├── source-pane.pper │ │ ├── windowlayoutstate.pper │ │ └── workbench-pane.pper │ │ ├── saved_source_markers │ │ └── sdb │ │ ├── prop │ │ ├── 30124030 │ │ ├── 1130D7E5 │ │ ├── 1D196447 │ │ ├── 72D0CCC4 │ │ ├── 7F78F386 │ │ ├── 8762AEFE │ │ ├── ADE46341 │ │ ├── AEBF0EBC │ │ ├── C279B592 │ │ ├── C5D1B627 │ │ ├── E57DA388 │ │ ├── E8B21E47 │ │ ├── EA820E90 │ │ ├── EEE0DCE1 │ │ ├── F84491F2 │ │ ├── FF3806ED │ │ └── INDEX │ │ └── s-DFAADFDB │ │ ├── CC5178A4 │ │ └── lock_file ├── metacc │ ├── .Rhistory │ ├── README.txt │ ├── annotate.R │ ├── assign_strand.R │ ├── binarise.R │ ├── merge.R │ ├── merge_sites.R │ ├── old │ │ ├── allele_specific │ │ │ ├── allele_regions.csv │ │ │ ├── merge_alleles.R │ │ │ └── merge_alleles2.R │ │ ├── assign_strand_old.R │ │ ├── binarise_old.R │ │ └── bulk.R │ ├── parsed_filter.R │ ├── pseudobulk_metacc.R │ ├── raw_filter.R │ ├── raw_filter.sh │ └── regress_PC.R └── rna │ ├── .DS_Store │ ├── .Rhistory │ ├── download.sh │ ├── featureCounts.R │ ├── preproc_rna.Rmd │ ├── pseudobulk_rna.R │ ├── regress_PC.R │ └── rename.sh ├── pseudobulk_profiles ├── .DS_Store ├── .Rhistory ├── pseudobulk_metacc │ ├── .DS_Store │ ├── .Rhistory │ ├── metacc_profiles.Rmd │ └── run.R ├── pseudobulk_metaccrna │ ├── .DS_Store │ ├── .Rhistory │ ├── metaccrna_profiles.Rmd │ └── run.R └── singlecell_acc_profiles │ ├── .DS_Store │ ├── data │ └── README.txt │ └── sc_profiles.Rmd ├── stats ├── .DS_Store ├── .Rhistory ├── features │ ├── .DS_Store │ ├── .Rhistory │ ├── stats_accmet_features_parsed.Rmd │ └── stats_accmet_features_parsed.html └── samples │ ├── .DS_Store │ ├── .Rhistory │ ├── cor_raw.Rmd │ ├── run.R │ └── stats_accmet_samples_raw.Rmd └── variance └── background_variance.Rmd /EB_cells/QC/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PMBio/scNMT-seq/HEAD/EB_cells/QC/.DS_Store -------------------------------------------------------------------------------- /EB_cells/QC/QC_accmet.Rmd: 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