Package Recipe 'bioconductor-stdeconvolve'

recipe bioconductor-stdeconvolve

Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/STdeconvolve.html
License:: GPL-3
Recipe:: /bioconductor-stdeconvolve/meta.yaml

STdeconvolve as an unsupervised, reference-free approach to infer latent cell-type proportions and transcriptional profiles within multi-cellular spatially-resolved pixels from spatial transcriptomics (ST) datasets. STdeconvolve builds on latent Dirichlet allocation (LDA), a generative statistical model commonly used in natural language processing for discovering latent topics in collections of documents. In the context of natural language processing, given a count matrix of words in documents, LDA infers the distribution of words for each topic and the distribution of topics in each document. In the context of ST data, given a count matrix of gene expression in multi-cellular ST pixels, STdeconvolve applies LDA to infer the putative transcriptional profile for each cell-type and the proportional representation of each cell-type in each multi-cellular ST pixel.

package bioconductor-stdeconvolve¶

Versions:

1.2.0-0

Depends:

on bioconductor-biocparallel >=1.32.0,<1.33.0
on r-base >=4.2,<4.3.0a0
on r-clue
on r-ggplot2
on r-liger
on r-matrix
on r-mgcv
on r-reshape2
on r-scatterpie
on r-slam
on r-topicmodels
on r-viridis

Additional platforms:

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-stdeconvolve

to add into an existing workspace instead, run:

pixi add bioconductor-stdeconvolve

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-stdeconvolve

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-stdeconvolve

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-stdeconvolve:<tag>

(see bioconductor-stdeconvolve/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-stdeconvolve/README.html)