Package Recipe 'bioconductor-scruff'

recipe bioconductor-scruff

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Homepage: https://bioconductor.org/packages/3.12/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

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

Depends

bioconductor-annotationdbi >=1.52.0,<1.53.0
bioconductor-biocgenerics >=0.36.0,<0.37.0
bioconductor-biocparallel >=1.24.0,<1.25.0
bioconductor-biostrings >=2.58.0,<2.59.0
bioconductor-genomeinfodb >=1.26.0,<1.27.0
bioconductor-genomicalignments >=1.26.0,<1.27.0
bioconductor-genomicfeatures >=1.42.0,<1.43.0
bioconductor-genomicranges >=1.42.0,<1.43.0
bioconductor-ggbio >=1.38.0,<1.39.0
bioconductor-rsamtools >=2.6.0,<2.7.0
bioconductor-rsubread >=2.4.0,<2.5.0
bioconductor-rtracklayer >=1.50.0,<1.51.0
bioconductor-s4vectors >=0.28.0,<0.29.0
bioconductor-shortread >=1.48.0,<1.49.0
bioconductor-singlecellexperiment >=1.12.0,<1.13.0
bioconductor-summarizedexperiment >=1.20.0,<1.21.0
r-base >=4.0,<4.1.0a0
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)