Man pages for keshav-motwani/scanalysis
Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data
| annotate_ambient_profile | Add average of ambient feature reads to rowData |
| annotate_cdr3 | Annotate CDR3 sequences stored in colData(sce)$vdj based on a... |
| annotate_chain_count | Annotate number of TRA, TRB, IGL, IGK, and IGH reads per... |
| annotate_clonotype_count | Annotate number of occurrences of a given clonotype in a... |
| annotate_n_cells_expr | Add number of cells with nonzero expression for each gene to... |
| annotate_n_genes_expr | Add number of genes expressed per barcode to... |
| annotate_pct_gene_set | Add percent of gene set defined by a regular expression... |
| annotate_pct_total_reads | Add percentage of total reads that each gene takes up across... |
| annotate_total_umi_count | Add number of total umis per barcode to... |
| assign_clonotypes | Function to use for assigning clonotypes based on custom... |
| cache | Cache and retrieve intermediate steps if path exists |
| compute_evenness_profile_long | Compute tidied data frame of evenness profiles per group... |
| compute_evenness_profile_matrix | Compute matrix of evenness profiles per group based on... |
| convert_identity_frequency_matrix_to_long | Convert an identity frequency matrix |
| dot-encode_identity_frequency_matrix | Helper function to encode identity frequency matrix given... |
| dot-filter_ambient_barcode_cellranger | Get filter for cells based on inflection point |
| dot-filter_ambient_barcode_empty_drops | Get filter for cells based on emptyDrops algorithm |
| dot-filter_ambient_barcode_inflection | Get filter for cells based on inflection point |
| dot-filter_ambient_barcode_knee | Get filter for cells based on knee point |
| dot-get_cell_annotations | Get cell annotations for feature_heatmap |
| dot-get_cell_features_assay | Get feature from assay (from alternate experiment) |
| dot-get_cell_features_assay_explicit_exp | Get feature from assay (from alternate experiment) |
| dot-get_cell_features_coldata | Get feature from column metadata |
| dot-get_cell_features_reduced_dimensions | Get feature from reduced dimensional representation |
| dot-get_feature_annotations | Get feature annotations for feature_heatmap |
| dot-get_reduced_dims | Get reduced dimensions of object |
| dot-prepare_barcode_counts | Prepare count annotations for number of cells passing each... |
| dot-prepare_barcode_cutoffs | Prepare cutoff values for each method |
| dot-prepare_barcode_plot_data | Prepare data for plotting barcode QC plot |
| dot-prepare_gex_bivariate_counts | Prepare counts of cells that meet filter criteria to annotate... |
| dot-prepare_gex_data | Prepare data frame to plot for gene expression related QC... |
| dot-prepare_gex_scale_limits | Prepare the limits of plot scale |
| dot-prepare_gex_univariate_counts | Prepare counts of cells that meet filter criteria to annotate... |
| dot-prepare_volcano_annotations | Prepare annotations for volcano plot |
| dot-read_10x_gene_expr | Read gene expression matrix from 10X data |
| dot-read_10x_vdj | Read VDJ information from 10X data |
| dot-sce_to_assay | Convert SingleCellExperiment object to Seurat assay |
| dot-seurat_assay_to_sce | Convert Seurat assay to SingleCellExperiment |
| encode_cell_identity_frequency_long | Encode frequencies of (combinations) of values in columns... |
| encode_cell_identity_frequency_matrix | Encode frequencies of (combinations) of values in columns... |
| encode_vdj_identity_frequency_long | Encode frequencies of (combinations) of values in columns... |
| encode_vdj_identity_frequency_matrix | Encode frequencies of (combinations) of values in columns... |
| filter_ambient_barcode | Get filter to remove ambient RNA barcodes based on the... |
| filter_n_genes_expr | Get filter for number of genes expressed per barcode based on... |
| filter_pct_mito | Get filter for percentage of mitochondrial reads expressed... |
| filter_total_umi | Get filter for total umis per barcode based on log... |
| filter_vdj_chain_count | Get filter for barcodes based on the number of chains for... |
| get_assay_data | Get assay data from either the main experiment or altExps |
| get_cell_features | Get feature from assay data, colData, or reducedDims at once... |
| get_multi_sample_pbmc_10k | Get modified version of PBMC 10k data from 10X |
| get_pbmc_5k_nextgem | Get PBMC 5k data using v3 chemistry |
| get_pbmc_5k_v3 | Get PBMC 5k data using v3 chemistry |
| get_row_data | Get rowData from either the main experiment or altExps |
| pipe | Pipe operator |
| plot_barcode_qc | QC plot of UMI rank vs total number of UMIs per barcode |
| plot_feature_distributions | Plot feature distributions from SingleCellExperiment objects |
| plot_feature_heatmap | Plot heatmap of features across cells with annotations |
| plot_gex_bivariate_qc | Scatterplot of two features of interest from colData with... |
| plot_gex_univariate_qc | Scatterplot of two features of interest from colData with... |
| plot_pairwise_features | Plot pairwise scatterplot of cell-level data |
| plot_reduced_dimensions | Plot reduced dimensional plot with multiple features |
| plot_vdj_gex_univariate_qc | Scatterplot of two features of interest from colData with... |
| plot_volcano | Plot volcano plot with annotations |
| read_10x | Read 10X gene expression and VDJ data into a... |
| sce_to_seurat | Convert SingleCellExperiment object to Seurat and retain... |
| select_top_de_genes | Select the top DE genes, ranked on either fold change or... |
| seurat_to_sce | Convert Seurat object to SingleCellExperiment and retain... |
| unnest_vdj | Get VDJ data with cell-level metadata |
