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/3.9/bioc/html/scPipe.html

License

GPL (>= 2)

Recipe

/bioconductor-scpipe/meta.yaml

package bioconductor-scpipe

(downloads) docker_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>)