recipe bioconductor-citefuse

CiteFuse: multi-modal analysis of CITE-seq data






CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

package bioconductor-citefuse

(downloads) docker_bioconductor-citefuse



depends bioconductor-rhdf5:


depends bioconductor-rhdf5:


depends bioconductor-s4vectors:


depends bioconductor-s4vectors:


depends bioconductor-scran:


depends bioconductor-scran:


depends bioconductor-singlecellexperiment:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends bioconductor-summarizedexperiment:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-compositions:

depends r-cowplot:

depends r-dbscan:

depends r-ggplot2:

depends r-ggraph:

depends r-ggridges:

depends r-gridextra:

depends r-igraph:

depends r-matrix:

depends r-mixtools:

depends r-pheatmap:

depends r-randomforest:

depends r-rcpp:

depends r-reshape2:

depends r-rlang:

depends r-rtsne:

depends r-scales:

depends r-uwot:



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-citefuse

and update with::

   mamba update bioconductor-citefuse

To create a new environment, run:

mamba create --name myenvname bioconductor-citefuse

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-citefuse/tags`_ for valid values for ``<tag>``)

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