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 bioconductor-biocparallel:

>=1.32.0,<1.33.0

depends r-base:

>=4.2,<4.3.0a0

depends r-clue:

depends r-ggplot2:

depends r-liger:

depends r-matrix:

depends r-mgcv:

depends r-reshape2:

depends r-scatterpie:

depends r-slam:

depends r-topicmodels:

depends r-viridis:

requirements:

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-stdeconvolve

and update with::

   mamba update bioconductor-stdeconvolve

To create a new environment, run:

mamba create --name myenvname bioconductor-stdeconvolve

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 quay.io/biocontainers/bioconductor-stdeconvolve:<tag>

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

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