recipe r-monocle3

An analysis toolkit for single-cell RNA-seq.

Homepage:

https://cole-trapnell-lab.github.io/monocle3/

Developer docs:

https://github.com/cole-trapnell-lab/monocle3

License:

MIT

Recipe:

/r-monocle3/meta.yaml

package r-monocle3

versions:

1.3.1-0,  1.0.0-5,  1.0.0-4,  1.0.0-3,  1.0.0-2,  1.0.0-1,  1.0.0-0,  0.2.3-1,  0.2.3-0, 

1.3.1-0,  1.0.0-5,  1.0.0-4,  1.0.0-3,  1.0.0-2,  1.0.0-1,  1.0.0-0,  0.2.3-1,  0.2.3-0,  0.2.2-0,  0.2.1-1,  0.2.1-0,  0.2.0-1,  0.2.0-0,  0.1.3-0

depends bioconductor-batchelor:

depends bioconductor-biobase:

depends bioconductor-biocgenerics:

>=0.28

depends bioconductor-delayedarray:

>=0.8

depends bioconductor-delayedmatrixstats:

>=1.4

depends bioconductor-hdf5array:

depends bioconductor-limma:

>=3.38.3

depends bioconductor-s4vectors:

depends bioconductor-singlecellexperiment:

depends bioconductor-summarizedexperiment:

>=1.11.5

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends r-assertthat:

>=0.2.1

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

>=0.8.0.1

depends r-ggplot2:

>=3.1.1

depends r-ggrastr:

depends r-ggrepel:

>=0.8.1

depends r-grr:

depends r-htmlwidgets:

>=1.3

depends r-igraph:

>=1.2.4

depends r-irlba:

>=2.3.3

depends r-knitr:

depends r-leidenbase:

depends r-lme4:

depends r-lmtest:

>=0.9_36

depends r-mass:

>=7.3_51.4

depends r-matrix:

>=1.2_17

depends r-matrix.utils:

depends r-pbapply:

>=1.4

depends r-pbmcapply:

>=1.4.1

depends r-pheatmap:

depends r-plotly:

>=4.9

depends r-plyr:

>=1.8.4

depends r-proxy:

>=0.4_23

depends r-pryr:

>=0.1.4

depends r-pscl:

>=1.5.2

depends r-purrr:

>=0.3.2

depends r-rann:

>=2.6.1

depends r-rcpp:

>=1.0.1

depends r-rcppparallel:

depends r-reshape2:

>=1.4.3

depends r-reticulate:

>=1.11.1

depends r-rhpcblasctl:

depends r-rmarkdown:

depends r-rsample:

>=0.0.5

depends r-rtsne:

>=0.15

depends r-shiny:

depends r-slam:

>=0.1_45

depends r-spdep:

>=1.1_2

depends r-speedglm:

>=0.3_2

depends r-spelling:

depends r-stringr:

>=1.4

depends r-testthat:

>=2.1

depends r-tibble:

>=2.1.1

depends r-tidyr:

>=0.8.3

depends r-uwot:

>=0.1.3

depends r-viridis:

>=0.5.1

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 r-monocle3

and update with::

   mamba update r-monocle3

To create a new environment, run:

mamba create --name myenvname r-monocle3

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/r-monocle3:<tag>

(see `r-monocle3/tags`_ for valid values for ``<tag>``)

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