Each folder contains an individual pipeline with dedicated REnv/Conda (renv or yaml) environments to ensure compatability.
| Pipeline | Language | Data Type | OS |
|---|---|---|---|
| Automated_Annotation | R/Py(Reticulate) | scRNA |    |
| Microarray_Analysis | R | Microarray/Bulk RNA | |
| CellChat_Single | R/Py(Reticulate) | scRNA | |
| CellChat_Comparison | R/Py(Reticulate) | scRNA | |
| SIGNET_Pipeline | Py | scRNA | |
| Alignment_Pipeline | Py/R | RNA/scRNA | |
| scATAC_Pipeline | R | scATAC | |
| CellOracle_Pipeline | Py | scRNA/scATAC | |
| CellRank_Pipeline | Py | scRNA | |
Tip
Pipeline quick summarization:
-
Alignment_Pipeline: Automated Kallisto|Bustools sequence alignment. Contains R based Droplet removal for droplet-based sequence methods. Requires FASTQ files as input.
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Automated_Annotation: Pseudo-automated annotation of Hair/Skin scRNA datasets using Adjusted Iterative Latent Semantic Idexing (LSI). Requires MTX, H5, 10x as input.
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Microarray_Analysis: Simple automated Microarray/RNA preprocessing and analysis using Oligo and GAGE. Requires Microarray (CEL) or batch RNA seq as input.
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CellChat_Single: infers intercellular communication. Runs a standard CellChat pipeline on a single annotated scRNA dataset. Requires Seurat object as input.
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CellChat_Comparison: infers intercellular communication. Runs a comparison CellChat pipeline between multiple scRNA datasets. Requires Seurat object(s) as input.
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SIGNET_Pipeline: Infers intracellular communication. Runs a SIGNET pipeline to establish transcriptional network using MLP training model. Requires raw expression matrix as input.
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scATAC_Pipeline: Uses ArchR and Cicero to generate GRNs for the purpose of CellOracle pertubartion analysis. Can modify ArchR to annotate scATAC data easily.
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CellOracle_Pipeline: Uses CellOracle and customizable GRNs from scATAC_Pipeline to perform gene perturbation analysis on scRNA dataset to track lineage changes.
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CellRank_Pipeline: Uses Palentir pseudotime and CellRank for Unified fate mapping in multiview single-cell data
Important
Important minimum prerequisites:
Download and install R (4.3.2+): https://www.r-project.org/
Download and install RTools (4.3+): https://cran.r-project.org/bin/windows/Rtools/
Download and install RStudio (3.3+): https://posit.co/download/rstudio-desktop/
Download and install Python (3.11+): https://www.python.org/downloads/
Download and install Microsoft C++ Build Tools: https://visualstudio.microsoft.com/visual-cpp-build-tools/
(In the Visual Studio Installer make sure to highlight the Desktop development with C++ and from Individual Components the Windows 11 or Windows 10 SDK)
For iOS users:
Download and install XQuartz https://www.xquartz.org/
Download and install XCode https://developer.apple.com/xcode/