- recipe bioconductor-scpipe
pipeline for single cell RNA-seq data analysis
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/scPipe.html
- License:
GPL (>= 2)
- Recipe:
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.
- package bioconductor-scpipe¶
-
- Versions:
1.19.0-0
,1.16.1-0
,1.16.0-1
,1.16.0-0
,1.14.0-0
,1.12.0-1
,1.12.0-0
,1.10.0-0
,1.8.0-0
,1.19.0-0
,1.16.1-0
,1.16.0-1
,1.16.0-0
,1.14.0-0
,1.12.0-1
,1.12.0-0
,1.10.0-0
,1.8.0-0
,1.6.0-1
,1.4.1-0
,1.4.0-0
,1.2.1-0
,1.0.0-0
- Depends:
bioconductor-annotationdbi
>=1.60.0,<1.61.0
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-biomart
>=2.54.0,<2.55.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-org.hs.eg.db
>=3.16.0,<3.17.0
bioconductor-org.mm.eg.db
>=3.16.0,<3.17.0
bioconductor-rhtslib
>=2.0.0,<2.1.0
bioconductor-rtracklayer
>=1.58.0,<1.59.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-scater
>=1.26.0,<1.27.0
bioconductor-singlecellexperiment
>=1.20.0,<1.21.0
bioconductor-summarizedexperiment
>=1.28.0,<1.29.0
bioconductor-zlibbioc
>=1.44.0,<1.45.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
libstdcxx-ng
>=12
r-base
>=4.2,<4.3.0a0
r-glue
>=1.3.0
r-rcpp
>=0.11.3
- Required By:
Installation
With an activated Bioconda channel (see 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-scpipe/README.html)