-
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
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
- 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:
[](http://bioconda.github.io/recipes/bioconductor-scruff/README.html)