All functions

aggregate_sparse_features aggregate_sparse_replicates

Aggregate sparse matrix operations

barcode_metrics

Generate barcode metrics summary

bcbioSinglecell-package

bcbioSinglecell

downloads

File downloads

filter_cellular_barcodes

Filter cellular barcodes

load_run

Load bcbio-nextgen run

metadata_table

Metadata table for knit report.

plot_barcode plot_barcodes

Sample barcode distribution quality control plots

plot_total_cells plot_total_counts_histogram plot_total_counts_boxplot plot_genes_detected_boxplot plot_genes_detected_histogram plot_total_vs_detected plot_mito_histogram plot_mito_boxplot plot_mito_scatterplot plot_novelty_histogram plot_novelty_boxplot plot_total_counts plot_genes_detected plot_mito plot_novelty

Cell metrics quality control plots

read_10x_counts

Read 10x Genomics Chromium output

read_bcbio_counts

Read bcbio-nextgen output

write_counts

Write MatrixMart sparse matrix and supporting files to disk