Dataset

Four pairs of Real Datasets (processed) and the downsampled datasets mentioned in the manuscript are available through: https://drive.google.com/drive/folders/1M0xS2pSX06AF9NwMUTCd9G-n-LuLHqCw?usp=sharing

Simulation Datasets

Please find the corresponding Rscripts for simulation data.

Run the Rscripts with Docker

Pull the software versions used in the manuscript from the Docker file (Here illustrate the use with Singularity).

usage in R session

The link to the docker image containing tools used in the paper with version control: https://hub.docker.com/r/qhhuang/benchmark_celltype_r_packages.

SINGULARITY_DOCKER_USERNAME=dockerusername SINGULARITY_DOCKER_PASSWORD=dockerpassword singularity pull docker://qhhuang/benchmark_celltype_r_packages:versioncontrol
singularity exec -B /path/to/your/working/directory /path/to/docker/img/benchmark_celltype_r_packages-versioncontrol.simg R

Then, proceeds your analysis as usual.

execute Rscript directly

singularity exec -B /path/to/your/working/directory /path/to/docker/img/benchmark_celltype_r_packages-versioncontrol.simg Rscript /path/to/your/Rscript/sample.R

Link to Softwares

For the information of software updates, please go to their corresponding pages.
Seurat [Recently updated Version 4 which allows multi-modal integration+transfered learning]
SingleR [Recently Add Rejection Option]
scmap
Garnett [Recently Add Automatic Marker Detection]
CHETAH
SCINA
singleCellNet
scID

Reference

Q. Huang, Y. Liu, Y. Du, L.X. Garmire, Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data, Genomics, Proteomics & Bioinformatics (2020), doi: https://doi.org/10.1016/j.gpb.2020.07.004.