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"QC_metrics<-", "QC_metrics<-,SingleCellExperiment-method" ] }, { "page": "read_cells", "title": "Read Cell barcode file", "topics": [ "read_cells" ] }, { "page": "remove_outliers", "title": "Remove outliers in 'SingleCellExperiment'", "topics": [ "remove_outliers" ] }, { "page": "sc_aligning", "title": "aligning the demultiplexed FASTQ reads using the Rsubread:align()", "topics": [ "sc_aligning" ] }, { "page": "sc_atac_bam_tagging", "title": "BAM tagging", "topics": [ "sc_atac_bam_tagging" ] }, { "page": "sc_atac_cell_calling", "title": "identifying true vs empty cells", "topics": [ "sc_atac_cell_calling" ] }, { "page": "sc_atac_create_cell_qc_metrics", "title": "generating a file useful for producing the qc plots", "topics": [ "sc_atac_create_cell_qc_metrics" ] }, { "page": "sc_atac_create_fragments", "title": "Generating the popular fragments for scATAC-Seq data", "topics": [ "sc_atac_create_fragments" ] }, { "page": "sc_atac_create_report", "title": "HTML report generation", "topics": [ "sc_atac_create_report" ] }, { "page": "sc_atac_create_sce", "title": "sc_atac_create_sce()", "topics": [ "sc_atac_create_sce" ] }, { "page": "sc_atac_emptydrops_cell_calling", "title": "empty drops cell calling", "topics": [ "sc_atac_emptydrops_cell_calling" ] }, { "page": "sc_atac_feature_counting", "title": "generating the feature by cell matrix", "topics": [ "sc_atac_feature_counting" ] }, { "page": "sc_atac_filter_cell_calling", "title": "filter cell calling", "topics": [ "sc_atac_filter_cell_calling" ] }, { "page": "sc_atac_peak_calling", "title": "sc_atac_peak_calling()", "topics": [ "sc_atac_peak_calling" ] }, { "page": "sc_atac_pipeline", "title": "A convenient function for running the entire pipeline", "topics": [ "sc_atac_pipeline" ] }, { "page": "sc_atac_pipeline_quick_test", "title": "A function that tests the pipeline on a small test sample (without duplicate removal)", "topics": [ "sc_atac_pipeline_quick_test" ] }, { "page": "sc_atac_plot_cells_per_feature", "title": "A histogram of the log-number of cells per feature", "topics": [ "sc_atac_plot_cells_per_feature" ] }, { "page": "sc_atac_plot_features_per_cell", "title": "A histogram of the log-number of features per cell", "topics": [ "sc_atac_plot_features_per_cell" ] }, { "page": "sc_atac_plot_features_per_cell_ordered", "title": "Plot showing the number of features per cell in ascending order", "topics": [ "sc_atac_plot_features_per_cell_ordered" ] }, { "page": "sc_atac_plot_fragments_cells_per_feature", "title": "A scatter plot of the log-number of fragments and log-number of cells per feature", "topics": [ "sc_atac_plot_fragments_cells_per_feature" ] }, { "page": "sc_atac_plot_fragments_features_per_cell", "title": "A scatter plot of the log-number of fragments and log-number of features per cell", "topics": [ "sc_atac_plot_fragments_features_per_cell" ] }, { "page": "sc_atac_plot_fragments_per_cell", "title": "A histogram of the log-number of fragments per cell", "topics": [ "sc_atac_plot_fragments_per_cell" ] }, { "page": "sc_atac_plot_fragments_per_feature", "title": "A histogram of the log-number of fragments per feature", "topics": [ "sc_atac_plot_fragments_per_feature" ] }, { "page": "sc_atac_remove_duplicates", "title": "Removing PCR duplicates using samtools", "topics": [ "sc_atac_remove_duplicates" ] }, { "page": "sc_atac_tfidf", "title": "generating the UMAPs for sc-ATAC-Seq preprocessed data", "topics": [ "sc_atac_tfidf" ] }, { "page": "sc_atac_trim_barcode", "title": "demultiplex raw single-cell ATAC-Seq fastq reads", "topics": [ "sc_atac_trim_barcode" ] }, { "page": "sc_correct_bam_bc", "title": "sc_correct_bam_bc", "topics": [ "sc_correct_bam_bc" ] }, { "page": "sc_count_aligned_bam", "title": "sc_count_aligned_bam", "topics": [ "sc_count_aligned_bam" ] }, { "page": "sc_demultiplex", "title": "sc_demultiplex", "topics": [ "sc_demultiplex" ] }, { "page": "sc_demultiplex_and_count", "title": "sc_demultiplex_and_count", "topics": [ 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