Supplementary Materials for scMaSigPro: Differential Expression Analysis along Single Cell Trajectories

This repository contains the supplementary material for the [scMaSigPro: Differential Expression Analysis along Single Cell Trajectories], which details our evaluation, benchmarks and analysis.

Docker

The docker container to re-run all the analysis can be found on DockerHub

Directory Structure

1. Directory 'benchmarks': Scripts for used to benchmark scMaSigPro can be found in this directory.

benchmarks
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    +--00_Parameter_Estimation: Splatter script to estimate parameters from real dataset.
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    +--01_Sparsity: Evaluation of datasets with increasing Sparsity.
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    +--02_Skewness: Evaluation of datasets with heterogeneous distribution of cells along the branching paths.
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    +--03_Different_length: Evaluation of datasets with different lengths of the branching paths.

comparison
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    +--01_ComparisonWithTradeSeq: Rscripts to compare with tradeSeq.
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    +--02_SpeedTimeComparisonWithTradeSeq: Time Comparison with tradeSeq.
    
analysis_public_data
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    +--01_Raw_to_processed.r: Raw counts to processed counts.
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    +--02_Cell_Type_Annotation.R: Cell Type inference with Azimuth.
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    +--03_SubSampling: SubSampling based on cell types.
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    +--04_TI_Monocle3.R: Trajectory inference with monocle3.
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    +--04.1_ScMaSigPro_Input.R: Selection of branhcing paths.
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    +--05_scMaSigPro.R: ScMaSigPro Analysis.
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    +--06_Exploration.R: GO enrichment.

Rscripts
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    +--combine: Rscripts to combine figures and tables for manuscript.
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    +--helper_function: Additional function.