- recipe bioconductor-scruff
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
- Homepage:
https://bioconductor.org/packages/3.14/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:
1.12.0-0
,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
>=1.56.0,<1.57.0
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicalignments
>=1.30.0,<1.31.0
bioconductor-genomicfeatures
>=1.46.0,<1.47.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-ggbio
>=1.42.0,<1.43.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-rsubread
>=2.8.0,<2.9.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-shortread
>=1.52.0,<1.53.0
bioconductor-singlecellexperiment
>=1.16.0,<1.17.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
r-base
>=4.1,<4.2.0a0
- Required By:
Installation
With an activated Bioconda channel (see 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-scruff/README.html)