campbio/scruff: Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.
Getting started
Browse package contents
Package details |
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| Bioconductor views | Alignment ImmunoOncology Preprocessing QualityControl RNASeq Sequencing SingleCell Software Technology Visualization WorkflowStep |
| Maintainer | |
| License | MIT + file LICENSE |
| Version | 1.21.1 |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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