bioconda / packages / bioconductor-slalom 1.16.0

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Installers

Info: This package contains files in non-standard labels.

conda install

  • linux-64  v1.16.0
  • osx-64  v1.16.0
To install this package run one of the following:
conda install -c bioconda bioconductor-slalom
conda install -c "bioconda/label/gcc7" bioconductor-slalom

Description

slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors. The method uses Bayesian factor analysis with a latent variable model to identify active pathways (selected by the user, e.g. KEGG pathways) that explain variation in a single-cell RNA-seq dataset. This an R/C++ implementation of the f-scLVM Python package. See the publication describing the method at https://doi.org/10.1186/s13059-017-1334-8.


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