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

Versions

1.2.4-0, 1.0.1-1, 1.0.1-0

Depends

• bioconductor-annotationdbi >=1.46.0,<1.47.0

• bioconductor-biocgenerics >=0.30.0,<0.31.0

• bioconductor-biocparallel >=1.18.0,<1.19.0

• bioconductor-biostrings >=2.52.0,<2.53.0

• bioconductor-genomeinfodb >=1.20.0,<1.21.0

• bioconductor-genomicalignments >=1.20.0,<1.21.0

• bioconductor-genomicfeatures >=1.36.0,<1.37.0

• bioconductor-genomicranges >=1.36.0,<1.37.0

• bioconductor-ggbio >=1.32.0,<1.33.0

• bioconductor-rsamtools >=2.0.0,<2.1.0

• bioconductor-rtracklayer >=1.44.0,<1.45.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• bioconductor-shortread >=1.42.0,<1.43.0

• bioconductor-singlecellexperiment >=1.6.0,<1.7.0

• bioconductor-summarizedexperiment >=1.14.0,<1.15.0

• r-base >=3.6,<3.7.0a0

• r-data.table

• r-ggplot2

• r-ggthemes

• r-plyr

• r-scales

• r-stringdist

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>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-scruff/README.html)