recipe bioconductor-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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/scruff.html

License

MIT + file LICENSE

Recipe

/bioconductor-scruff/meta.yaml

package bioconductor-scruff

(downloads) docker_bioconductor-scruff

Versions

1.2.4-0, 1.0.1-1, 1.0.1-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-scruff

and update with:

conda update bioconductor-scruff

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-scruff:<tag>

(see bioconductor-scruff/tags for valid values for <tag>)