BunisHSPCData: Obtain the Bunis haematopoietic stem and progenitor cell data

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

Obtain the Bunis haematopoietic stem and progenitor cell data

Description

Obtain the human fetal, newborn, and adult haematopoietic stem and progenitor cell single-cell RNA-seq dataset from Bunis et al. (2021).

Usage

BunisHSPCData(filtered = TRUE, legacy = FALSE)

Arguments

filtered	Logical scalar or "cells" indicating whether to: TRUE: filter out cells that were not used by the authors. "cells": filter out empty droplets as filtered out by cell ranger. FALSE: no filtering
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

Details

Column metadata is recreated from GEO using the author-supplied TSV of per-cell annotations, or retrieved from a processed version of the data shared by authors via figshare. This contains information such as the tissue & sample of origin, age group, likely cell type, and Developmental Stage Scoring. Within DevStageScoring element of the column metadata are the applied results ('<cell_type>_scores') of random forest regression trained on the fetal (score = 0) and adult (score = 1) cells of individual cell types indicated by ('<cell_type>_inTraining').

If filtered=TRUE, only the cells used by the authors in their final analysis are returned. Otherwise, an additional retained field will be present in the colData, indicating whether the cell was retained by the authors.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/bunis-hspc.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Daniel Bunis

References

Bunis DG et al. (2021). Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells Cell Rep. 34(1): 108573

Examples

sce <- BunisHSPCData()

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.