recipe bioconductor-monocle

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq







biotools: monocle

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

package bioconductor-monocle

(downloads) docker_bioconductor-monocle



depends bioconductor-biobase:


depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-biocgenerics:


depends bioconductor-biocviews:


depends bioconductor-biocviews:


depends bioconductor-hsmmsinglecell:


depends bioconductor-hsmmsinglecell:


depends bioconductor-limma:


depends bioconductor-limma:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-cluster:

depends r-combinat:

depends r-ddrtree:


depends r-dplyr:

depends r-fastica:

depends r-ggplot2:


depends r-igraph:


depends r-irlba:


depends r-leidenbase:


depends r-mass:

depends r-matrix:


depends r-matrixstats:

depends r-pheatmap:

depends r-plyr:

depends r-proxy:

depends r-qlcmatrix:

depends r-rann:


depends r-rcpp:


depends r-reshape2:

depends r-rtsne:

depends r-slam:

depends r-stringr:

depends r-tibble:

depends r-vgam:


depends r-viridis:



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-monocle

and update with::

   mamba update bioconductor-monocle

To create a new environment, run:

mamba create --name myenvname bioconductor-monocle

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<tag>

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

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