if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SingleCellMultiModal")
This package introduces a suite of single-cell multimodal landmark datasets for
benchmarking and testing multimodal analysis methods via the
Bioconductor package. The scope of this package is to provide efficient access
to a selection of curated, pre-integrated, publicly available landmark datasets
for methods development and benchmarking.
Users can obtain integrative representations of multiple modalities as a
MultiAssayExperiment, a common core Bioconductor data structure relied on by
dozens of multimodal data analysis packages.
data management of multiple experimental assays performed on an overlapping set
of specimens. Although originally developed for patient data from multi-omics
cancer studies, the
MultiAssayExperiment framework naturally applies also to
single cells. A schematic of the data structure can be seen below. In this
context, “patients” are replaced by “cells”. We use
because it provides a familiar user experience by extending
SummarizedExperiment concepts and providing open ended compatibility with
standard data classes present in Bioconductor such as the
Ramos, Marcel, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, et al. 2017. “Software for the Integration of Multiomics Experiments in Bioconductor.” Cancer Res. 77 (21): e39–e42.