/scRNA_cell_deconv_benchmark

Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data

Primary LanguageR

Dataset

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

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

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
SingleR [Recently Add Rejection Option]
scmap
Garnett [Recently Add Automatic Marker Detection]
CHETAH
SCINA
singleCellNet
scID