scRNAIdent

Description

scRNAIdent provides a modularized R pipeline tool for automating the evaluation and comparison of cell typing methods in scRNA-seq analysis. The The workflow of the pipeline is illustrated in the picture below.

Pipeline modules

In brevity, the pipeline consists of seven modules. These modules are functionally independent and can be easily modified for adding new cell typing methods or evaluation metrics. The modules are described in the following subsections.

1. Configuration module

The configuration module consists of multiple configuration files. It specifies instructions for driving other modules and provides a means of communicating among modules. The components of the module is listed below.

Name	File	Description
Pipeline	config.R	Pipeline home path and various directories
Experiment	experiments_config.R	Parameters for driving experiment module. For example, experiment name, initial values experiment parameters, tested methods, used datasets, parameters of constructing experimental datasets, evaluation metrics, etc.
Method	methods_config.R	Methods hyperparameters
Dataset	dataset_config.R	Basic properties of datasets, lists of pairs of reference/query datasets
Marker gene	markergene_config.R	Parameters for marker gene selection method

2. Data preprocessor

This module preprocesses raw scRNA-seq datasets into SingleCellExperiment objects, performs basic QC, and calculates and adds corresponding metadata.

3. Experiment drive

This module is the central part of the pipeline. It coordinates the functioning of other modules, sending instructions and receiving outputs from each other module. Its functionalities include:

• Parsing and updating configurations for experimental instructions
• Sending instructions to dataset constructor and receiving constructed training/testing datasets.
• Sending training/testing datasets to method drive. Receiving classification/clustering results from methods.
• Sending datasets and results to analysis module. Receiving reports of dataset properties metrics and performance metrics.
• Sending performance reports to reporting module for saving and plotting.

4. Experimental dataset constructor

This module samples the reference/query datasets to construct the training/testing datasets based on received instructions from experiment drive.

5. Method drive

This module parses the method configurations and run the methods on received training/testing datasets based on specific experimental instructions from experiment drive.

6. Analysis module

This module receives training/testing datasets and classification/clustering results. It then calculates the analytical properties of the datasets, and performance metrics on the results.

7. Reporting module

This module dumps the performance results and plots various analytical figures.

Examples

To run the experiment of amount of cells

1. Specify the home, data and other relevant directories of the pipeline in config.R

    home <- '***'
    data_home <- '***'
    result_home <- '***'
    log_home <- '***'
    log_file <- "scRNAIdent.log"
    marker_home <- '***'
    type_home <- '***'
    pretrained_home <- '***'
    raw_data_home <- '***'
   

2. Specify the experimental parameters in the experiments_config.R

   • Set experiment name experiment <- "cell_number"

   • Set experimental methods and parameters

       experiments.methods <- list(cell_number=list(...))
       experiments.parameters <- list(cell_number=list(...))
     

   • (optional) If adding new experiment, implement experimental parameters initiating and updating functions

       experiments.config.init.cell_number <- function(train_dataset, test_dataset=NULL, exp_config)
       experiments.config.update.cell_number <- function(train_dataset, test_dataset=NULL, exp_config)
     

3. (optional) If testing new datasets, add to and update the configurations in the dataset_config.R

4. (optional) If testing a new method, add the new method to methods.R and its configurations to methods_config.R

5. (optional) If testing new marker gene selection methods, add the methods to marke_gene.R and its configurations to markergene_config.R

6. (optional) If using a new evaluation metric, add the metric calculating function to analysis.R and add the metric to the metrics parameter in the corresponding experiment configurations in experiments_config.R

7. load the experiments.R script and run

    runExperiments(experiment)