Package Recipe 'bioconductor-scruff'

recipe bioconductor-scruff

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Homepage: https://bioconductor.org/packages/3.11/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

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

Depends

bioconductor-annotationdbi >=1.50.0,<1.51.0
bioconductor-biocgenerics >=0.34.0,<0.35.0
bioconductor-biocparallel >=1.22.0,<1.23.0
bioconductor-biostrings >=2.56.0,<2.57.0
bioconductor-genomeinfodb >=1.24.0,<1.25.0
bioconductor-genomicalignments >=1.24.0,<1.25.0
bioconductor-genomicfeatures >=1.40.0,<1.41.0
bioconductor-genomicranges >=1.40.0,<1.41.0
bioconductor-ggbio >=1.36.0,<1.37.0
bioconductor-rsamtools >=2.4.0,<2.5.0
bioconductor-rsubread >=2.2.0,<2.3.0
bioconductor-rtracklayer >=1.48.0,<1.49.0
bioconductor-s4vectors >=0.26.0,<0.27.0
bioconductor-shortread >=1.46.0,<1.47.0
bioconductor-singlecellexperiment >=1.10.0,<1.11.0
bioconductor-summarizedexperiment >=1.18.0,<1.19.0
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)