Man pages for scruff
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
| 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... |
| countUMI | Count the number of UMIs for each gene and output count... |
| 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) |
