recipe bioconductor-scran

Methods for Single-Cell RNA-Seq Data Analysis

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/scran.html

License:

GPL-3.0-only

Recipe:

/bioconductor-scran/meta.yaml

Links:

biotools: scran

Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.

package bioconductor-scran

(downloads) docker_bioconductor-scran

versions:
1.30.0-11.30.0-01.28.1-01.26.0-11.26.0-01.22.1-11.22.1-01.22.0-01.20.1-0

1.30.0-11.30.0-01.28.1-01.26.0-11.26.0-01.22.1-11.22.1-01.22.0-01.20.1-01.18.5-01.18.0-01.16.0-01.14.1-01.14.0-01.12.1-01.10.1-01.8.4-01.6.2-01.4.5-0

depends bioconductor-beachmat:

>=2.18.0,<2.19.0

depends bioconductor-beachmat:

>=2.18.0,<2.19.0a0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-biocsingular:

>=1.18.0,<1.19.0

depends bioconductor-biocsingular:

>=1.18.0,<1.19.0a0

depends bioconductor-bluster:

>=1.12.0,<1.13.0

depends bioconductor-bluster:

>=1.12.0,<1.13.0a0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0a0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0a0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-edger:

>=4.0.16,<4.1.0a0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-limma:

>=3.58.1,<3.59.0a0

depends bioconductor-metapod:

>=1.10.0,<1.11.0

depends bioconductor-metapod:

>=1.10.0,<1.11.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends bioconductor-scuttle:

>=1.12.0,<1.13.0

depends bioconductor-scuttle:

>=1.12.0,<1.13.0a0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

depends r-dqrng:

depends r-igraph:

depends r-matrix:

depends r-rcpp:

depends r-statmod:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-scran

and update with::

   mamba update bioconductor-scran

To create a new environment, run:

mamba create --name myenvname bioconductor-scran

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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