- recipe bioconductor-citefuse
CiteFuse: multi-modal analysis of CITE-seq data
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/CiteFuse.html
- License:
GPL-3
- Recipe:
- Links:
biotools: citefuse
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¶
- versions:
1.18.0-0,1.14.0-1,1.14.0-0,1.12.0-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.2.0-0,1.18.0-0,1.14.0-1,1.14.0-0,1.12.0-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.2.0-0,1.0.0-0- depends bioconductor-rhdf5:
>=2.50.0,<2.51.0- depends bioconductor-rhdf5:
>=2.50.0,<2.51.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-scran:
>=1.34.0,<1.35.0- depends bioconductor-scran:
>=1.34.0,<1.35.0a0- depends bioconductor-singlecellexperiment:
>=1.28.0,<1.29.0- depends bioconductor-singlecellexperiment:
>=1.28.0,<1.29.0a0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=13- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx:
>=13- depends r-base:
>=4.4,<4.5.0a0- 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:
- requirements:
- additional platforms:
linux-aarch64
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-citefuse and update with:: mamba update bioconductor-citefuse
To create a new environment, run:
mamba create --name myenvname bioconductor-citefuse
with
myenvnamebeing 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-citefuse:<tag> (see `bioconductor-citefuse/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-citefuse/README.html)
