-
recipe
bioconductor-scpipe¶ A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.
- Homepage
- License
GPL (>= 2)
- Recipe
-
package
bioconductor-scpipe¶ 
- Versions
1.4.1-0, 1.4.0-0, 1.2.1-0, 1.0.0-0
- Depends bioconductor-annotationdbi
>=1.44.0,<1.45.0
- Depends bioconductor-biocgenerics
>=0.28.0,<0.29.0
- Depends bioconductor-biomart
>=2.38.0,<2.39.0
- Depends bioconductor-genomicranges
>=1.34.0,<1.35.0
- Depends bioconductor-org.hs.eg.db
>=3.7.0,<3.8.0
- Depends bioconductor-org.mm.eg.db
>=3.7.0,<3.8.0
- Depends bioconductor-rhtslib
>=1.14.0,<1.15.0
- Depends bioconductor-rtracklayer
>=1.42.0,<1.43.0
- Depends bioconductor-s4vectors
>=0.20.0,<0.21.0
- Depends bioconductor-singlecellexperiment
>=1.4.0,<1.5.0
- Depends bioconductor-summarizedexperiment
>=1.12.0,<1.13.0
- Depends bioconductor-zlibbioc
>=1.28.0,<1.29.0
- Depends libgcc-ng
>=7.3.0
- Depends libstdcxx-ng
>=7.3.0
- Depends r-base
>=3.5.1,<3.5.2.0a0
- Depends r-dplyr
- Depends r-ggally
- Depends r-ggplot2
- Depends r-glue
- Depends r-hashmap
- Depends r-magrittr
- Depends r-mass
- Depends r-mclust
- Depends r-rcpp
>=0.11.3
- Depends r-reshape
- Depends r-robustbase
- Depends r-scales
- Depends r-stringr
- Depends r-testthat
- Requirements
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-scpipe
and update with:
conda update bioconductor-scpipe
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-scpipe:<tag>
(see bioconductor-scpipe/tags for valid values for
<tag>)
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-scpipe/README.html)