-
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
- License
MIT + file LICENSE
- Recipe
-
package
bioconductor-scruff¶ 
- Versions
1.0.1-1, 1.0.1-0
- Depends bioconductor-annotationdbi
>=1.44.0,<1.45.0
- Depends bioconductor-biocgenerics
>=0.28.0,<0.29.0
- Depends bioconductor-biocparallel
>=1.16.0,<1.17.0
- Depends bioconductor-biostrings
>=2.50.0,<2.51.0
- Depends bioconductor-genomeinfodb
>=1.18.0,<1.19.0
- Depends bioconductor-genomicalignments
>=1.18.0,<1.19.0
- Depends bioconductor-genomicfeatures
>=1.34.0,<1.35.0
- Depends bioconductor-genomicranges
>=1.34.0,<1.35.0
- Depends bioconductor-ggbio
>=1.30.0,<1.31.0
- Depends bioconductor-rsamtools
>=1.34.0,<1.35.0
- Depends bioconductor-s4vectors
>=0.20.0,<0.21.0
- Depends bioconductor-shortread
>=1.40.0,<1.41.0
- Depends bioconductor-singlecellexperiment
>=1.4.0,<1.5.0
- Depends bioconductor-summarizedexperiment
>=1.12.0,<1.13.0
- Depends r-base
>=3.5.1,<3.5.2.0a0
- Depends r-data.table
- Depends r-ggplot2
- Depends r-ggthemes
- Depends r-plyr
- Depends r-refgenome
- Depends r-scales
- Depends r-stringdist
- Requirements
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:
[](http://bioconda.github.io/recipes/bioconductor-scruff/README.html)