Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Documentation for package ‘scruff’ version 1.5.12

alignRsubread	A wrapper to 'Rsubread' read alignment function 'align'
bamExample	Example GAlignments Object
barcodeExample	A vector of example cell barcodes.
cbtop10000	Top 10,000 rows for v1, v2, and v3 cell barcode whitelist files
countUMI	Count the number of UMIs for each gene and output count matrix
demultiplex	Demultiplex cell barcodes and assign cell specific reads
gview	Visualize gene isoforms
qcplots	Visualize data quality
rview	Visualize aligned reads
sceExample	Example SingleCellExperiment Object
scruff	Run scruff pipeline
tenxBamqc	Generate and output 10X read alignment data quality metrics
validCb	Cell barcode whitelist (737K-august-2016.txt)