- recipe bioconductor-aggregatebiovar
Differential Gene Expression Analysis for Multi-subject scRNA-seq
For single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates), this package contains tools to summarize single cell gene expression profiles at the level of subject. A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.
- package bioconductor-aggregatebiovar¶
- depends bioconductor-s4vectors:
- depends bioconductor-singlecellexperiment:
- depends bioconductor-summarizedexperiment:
- depends r-base:
- depends r-matrix:
- depends r-rlang:
- depends r-tibble:
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-aggregatebiovar and update with:: mamba update bioconductor-aggregatebiovar
To create a new environment, run:
mamba create --name myenvname bioconductor-aggregatebiovar
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-aggregatebiovar:<tag> (see `bioconductor-aggregatebiovar/tags`_ for valid values for ``<tag>``)