recipe bioconductor-scruff

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Homepage

https://bioconductor.org/packages/3.13/bioc/html/scruff.html

License

MIT + file LICENSE

Recipe

/bioconductor-scruff/meta.yaml

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.

package bioconductor-scruff

Versions

1.10.0-0,  1.8.3-0,  1.8.1-0,  1.6.0-0,  1.4.0-0,  1.2.4-0,  1.0.1-1,  1.0.1-0

Depends

• bioconductor-annotationdbi >=1.54.0,<1.55.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-ggbio >=1.40.0,<1.41.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rsubread >=2.6.0,<2.7.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-shortread >=1.50.0,<1.51.0

• bioconductor-singlecellexperiment >=1.14.0,<1.15.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• r-base >=4.1,<4.2.0a0

• 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)