This dataset contains the processed reference dataset from the HeOrganAtlas dataset for Marrow tissue. It has been preprocessed to include log-normalized counts, specific metadata columns, and PCA, t-SNE, and UMAP results.
reference_dataAn object of class SingleCellExperiment with 392 rows and 1500 columns.
The HeOrganAtlas dataset, available through the scRNAseq package.
This dataset underwent the following steps:
Loads the HeOrganAtlas dataset specifically for Marrow tissue from the scRNAseq package.
Divides the loaded dataset into a reference dataset used for downstream analysis.
Performs log normalization on the reference dataset using the function logNormCounts from the scuttle package.
Selects the column expert_annotation) from the cell metadata for downstream analysis.
Selects highly variable genes (HVGs) using the function getTopHVGs from the scran package on the reference dataset.
Performs Principal Component Analysis (PCA) on the reference dataset using the function runPCA from the scater package.
Performs t-Distributed Stochastic Neighbor Embedding (t-SNE) on the reference dataset using the function runTSNE from the scater package.
Performs Uniform Manifold Approximation and Projection (UMAP) on the reference dataset using the function runUMAP from the scater package.
He, et al. (2020). HeOrganAtlas: a comprehensive human organ atlas based on single-cell RNA sequencing.
Use data("reference_data") to load and access the resulting reference dataset.
# Load and explore the reference dataset
data("reference_data")