recipe bioconductor-scran

Implements functions for low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, detection of highly variable and significantly correlated genes, correction of batch effects, identification of marker genes, and other common tasks in single-cell analysis workflows.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/scran.html

License

GPL-3

Recipe

/bioconductor-scran/meta.yaml

Links

biotools: scran

package bioconductor-scran

(downloads) docker_bioconductor-scran

Versions

1.10.1-0, 1.8.4-0, 1.6.2-0, 1.4.5-0

Depends bioconductor-beachmat

>=1.4.0,<1.5.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-biocneighbors

>=1.0.0,<1.1.0

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-delayedarray

>=0.8.0,<0.9.0

Depends bioconductor-delayedmatrixstats

>=1.4.0,<1.5.0

Depends bioconductor-edger

>=3.24.0,<3.25.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-rhdf5lib

>=1.4.0,<1.5.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-scater

>=1.10.0,<1.11.0

Depends bioconductor-singlecellexperiment

>=1.4.0,<1.5.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends libgcc-ng

>=7.3.0

Depends libstdcxx-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-dynamictreecut

Depends r-igraph

Depends r-matrix

Depends r-rcpp

>=0.12.14

Depends r-statmod

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-scran

and update with:

conda update bioconductor-scran

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-scran:<tag>

(see bioconductor-scran/tags for valid values for <tag>)