Package Recipe 'bioconductor-celda'

recipe bioconductor-celda

CEllular Latent Dirichlet Allocation

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/celda.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-celda/meta.yaml

Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.

package bioconductor-celda¶

Versions:

1.26.0-0, 1.22.0-1, 1.22.0-0, 1.18.1-0, 1.16.1-0, 1.14.0-1, 1.14.0-0, 1.10.0-2, 1.10.0-1,

1.26.0-0, 1.22.0-1, 1.22.0-0, 1.18.1-0, 1.16.1-0, 1.14.0-1, 1.14.0-0, 1.10.0-2, 1.10.0-1, 1.10.0-0, 1.8.1-0, 1.6.1-1, 1.6.1-0, 1.4.5-0, 1.2.0-0, 1.0.4-0

Depends:

on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-complexheatmap >=2.26.1,<2.27.0a0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-delayedarray >=0.36.0,<0.37.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-scater >=1.38.0,<1.39.0a0
on bioconductor-scran >=1.38.0,<1.39.0
on bioconductor-scran >=1.38.0,<1.39.0a0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-data.table
on r-dbscan
on r-dendextend
on r-digest
on r-doparallel
on r-enrichr
on r-foreach
on r-ggdendro
on r-ggplot2
on r-ggrepel
on r-gridextra
on r-gtable
on r-matrix
on r-matrixstats
on r-mcmcprecision
on r-plyr
on r-proc
on r-rcolorbrewer
on r-rcpp
on r-rcppeigen
on r-reshape2
on r-rtsne
on r-scales
on r-stringr
on r-uwot
on r-withr

Additional platforms:

linux-aarch64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-celda

to add into an existing workspace instead, run:

pixi add bioconductor-celda

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-celda

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-celda

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

(see bioconductor-celda/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-celda/README.html)