Four pairs of Real Datasets (processed) and the downsampled datasets mentioned in the manuscript are available through: https://drive.google.com/drive/folders/1famn_tRVT_Es0GgFng508QggXcqETPCJ?usp=sharing
Please find the corresponding Rscripts for simulation data.
Pull the software versions used in the manuscript from the Docker file (Here illustrate the use with Singularity).
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.
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
For the information of software updates, please go to their corresponding pages.
Seurat
SingleR [Recently Add Rejection Option]
scmap
Garnett [Recently Add Automatic Marker Detection]
CHETAH
SCINA
singleCellNet
scID