Single Cell RNA-Seq UMI Filtering Facilitator (scruff)


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Documentation for package ‘scruff’ version 1.0.3

Help Pages

alignRsubread A wrapper to 'Rsubread' read alignment function 'align'
bamExample Example GAlignments Object
barcodeExample A vector of example cell barcodes.
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)