recipe bioconductor-scpipe

pipeline for single cell RNA-seq data analysis

Homepage

https://bioconductor.org/packages/3.11/bioc/html/scPipe.html

License

GPL (>= 2)

Recipe

/bioconductor-scpipe/meta.yaml

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

1.10.0-0,  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 >=1.50.0,<1.51.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biomart >=2.44.0,<2.45.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-org.hs.eg.db >=3.11.0,<3.12.0

• bioconductor-org.mm.eg.db >=3.11.0,<3.12.0

• bioconductor-rhtslib >=1.20.0,<1.21.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-scater >=1.16.0,<1.17.0

• bioconductor-singlecellexperiment >=1.10.0,<1.11.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• bioconductor-zlibbioc >=1.34.0,<1.35.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• libstdcxx-ng >=7.3.0

• r-base >=4.0,<4.1.0a0

• r-dplyr

• r-ggally

• r-ggplot2

• r-glue >=1.3.0

• r-hash

• r-magrittr

• r-mass

• r-mclust

• r-rcpp >=0.11.3

• r-reshape

• r-rlang

• 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:

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