recipe bioconductor-scpipe

pipeline for single cell RNA-seq data analysis

Homepage

https://bioconductor.org/packages/3.13/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

1.14.0-0,  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, 

1.14.0-0,  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 >=1.54.0,<1.55.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biomart >=2.48.0,<2.49.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-org.hs.eg.db >=3.13.0,<3.14.0

• bioconductor-org.mm.eg.db >=3.13.0,<3.14.0

• bioconductor-rhtslib >=1.24.0,<1.25.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-scater >=1.20.0,<1.21.0

• bioconductor-singlecellexperiment >=1.14.0,<1.15.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• bioconductor-zlibbioc >=1.38.0,<1.39.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.3.0

• r-base >=4.1,<4.2.0a0

• 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>)

Download stats

Link to this page

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