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scruff

This is the released version of scruff; for the devel version, see scruff.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

DOI: 10.18129/B9.bioc.scruff

Bioconductor version: Release (3.23)

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.

Author: Zhe Wang [aut, cre], Junming Hu [aut], Joshua Campbell [aut]

Maintainer: Zhe Wang <zhe at bu.edu>

Citation (from within R, enter citation("scruff")):

Zhe Wang, Junming Hu, Joshua Campbell. scruff: Single Cell RNA-Seq UMI Filtering Facilitator (scruff). doi:10.18129/B9.bioc.scruff, R package version 1.30.0, https://bioconductor.org/packages/scruff.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scruff")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scruff")

Details

Package Archives

Follow Installation instructions to use this package in your R session.