CellRef

Guided construction of single cell reference for human and mouse lung

Welcome to the development site of LungMAP CellRefs, single cell references with comprehensive and well-defined cell types for both human and mouse lungs.

The LungMAP CellRefs v1 were constructed using a new guided computational pipeline that utilized the LungMAP CellCards as a cell type dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples and identified 48 human and 40 mouse well-defined lung cell types catalogued from diverse anatomic locations and developmental time points. Please see details in the CellRef preprint. Code to reproduce the results in the CellRef manuscript is in the folder cellref_manuscript

Web interfaces to LungMAP CellRefs:

• LGEA CellRef interfaces: https://research.cchmc.org/pbge/lunggens/CellRef/LungMapCellRef.html
• LungMAP CellRef ShinyCell apps: https://app.lungmap.net/app/shinycell-human-lung-cellref
• LungMAP CellRef Azimuth instances: https://app.lungmap.net/app/azimuth-human-lung-cellref-seed
• LungMAP CellCards: https://lungmap.net/cell-cards/

Vignette:

• Demonstration of Guided CellRef construction using scRNA-seq of human lung endothelial cells lung_endo_vignette
• Demonstration of automated cell type annotation using CellRef cellref_annotation_demo

System requirements

CellRef has been tested on R versions >= 4.1 on Windows 10 64bit and macOS (Monterey) platforms. Please consult the DESCRIPTION file for more details on required R packages.

Installation

Install dependent R packages

install.packages(c("Seurat",'pheatmap','harmony','RobustRankAggreg','devtools','writexl','readxl','qpdf','ggpubr','gprofiler2'))

Install BioManager

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.15")

Install dependent BioConductor packages

BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'Matrix.utils',
                       'HDF5Array', 'terra', 'ggrastr', 'SingleR', 'scran'))

Install monocle3 (version 1.0.0)

devtools::install_github('cole-trapnell-lab/monocle3@1.0.0')

Install CellRef

devtools::install_github('xu-lab/CellRef')

Test CellRef installation

library(CellRef)