# Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

## Documentation for package ‘scruff’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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)