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

https://bioconductor.org/packages/3.8/bioc/html/scPipe.html

License

GPL (>= 2)

Recipe

/bioconductor-scpipe/meta.yaml

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

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-biomart >=2.38.0,<2.39.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-org.hs.eg.db >=3.7.0,<3.8.0

• bioconductor-org.mm.eg.db >=3.7.0,<3.8.0

• bioconductor-rhtslib >=1.14.0,<1.15.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-singlecellexperiment >=1.4.0,<1.5.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• bioconductor-zlibbioc >=1.28.0,<1.29.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.5.1,<3.5.2.0a0

• r-dplyr

• r-ggally

• r-ggplot2

• r-glue

• r-hashmap

• r-magrittr

• r-mass

• r-mclust

• r-rcpp >=0.11.3

• r-reshape

• r-robustbase

• r-scales

• r-stringr

• r-testthat

Required By

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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-scpipe/README.html)