BAIA Single Cell analysis ToolKit (BAIA-SCTK)

The BAIA Single Cell analysis ToolKit is a collection of interoperable R packages developed by the Bioinformatics and AI Applications (BAIA) Unit at the Institut Pasteur du Cambodge. The toolkit supports common single-cell RNA-seq analyses through a set of modular packages that can be used independently or combined into larger workflows.

Overview

The BAIA Single Cell analysis toolkit is modular. Some packages are commonly used together, while others can be applied independently depending on the biological question being addressed.

Package	Description
baia-seurat-helpers	Utilities for Seurat-based preprocessing, metadata management, visualization, and quality control.
baia-ext-cellprop-plots	Publication-quality cell composition and cell proportion analyses.
baia-cellchat	Simplified CellChat workflows for cell-cell communication analysis.
baia-pathway-analysis	Functional enrichment and pathway analysis tools for differential expression results.
baia-pseudobulk-deseq	Pseudobulk differential expression workflows based on DESeq2.

                               ┌─────────────────────┐
                               │ baia-seurat-helpers │
                               └──────────┬──────────┘
                                          │
             ┌────────────────────────────┼────────────────────────────┐
             │                            │                            │
             ▼                            ▼                            ▼

┌─────────────────────┐      ┌─────────────────────┐      ┌─────────────────────┐
│ Cell Composition    │      │ Differential        │      │ Cell Communication  │
│ Analysis            │      │ Expression          │      │ Analysis            │
│                     │      │                     │      │                     │
│ baia-ext-           │      │ baia-pseudobulk-    │      │ baia-cellchat       │
│ cellprop-plots      │      │ deseq               │      │                     │
└─────────────────────┘      └──────────┬──────────┘      └─────────────────────┘
                                         │
                                         ▼
                           ┌─────────────────────────┐
                           │ Pathway Enrichment      │
                           │                         │
                           │ baia-pathway-analysis   │
                           └─────────────────────────┘

Installation

Each package can be installed independently.

remotes::install_github("baia-ipc/baia-seurat-helpers")
remotes::install_github("baia-ipc/baia-ext-cellprop-plots")
remotes::install_github("baia-ipc/baia-cellchat")
remotes::install_github("baia-ipc/baia-pathway-analysis")
remotes::install_github("baia-ipc/baia-pseudobulk-deseq")

See the individual repositories for package-specific documentation and examples.

Use Cases

baia-ext-cellprop-plots: Cell Type Composition

Compare cell populations between conditions, cohorts, or time points.

Link: baia-ext-cellprop-plots

Input:

Seurat object with annotated cell types, after processing with sc-proportion-plots

Outputs:

Stacked barplots
Proportion plots
Statistical comparisons

baia-pseudobulk-deseq and baia-pathway-analysis: Differential Expression and Functional Interpretation

Identify transcriptional changes and their biological implications.

Links:

Typical workflow:

Seurat object
      ↓
Pseudobulk DESeq2
      ↓
Differentially expressed genes
      ↓
Pathway enrichment

baia-pathway-analysis can also be used independently with differential expression results generated by other tools.

baia-cellchat: Cell–Cell Communication

Study signaling interactions between cell populations.

Link: baia-cellchat

Input:

Annotated Seurat object

Outputs:

Interaction networks
Signaling pathway analyses
Comparative communication analyses

This package can be used independently of the differential expression and pathway-analysis workflows.

baia-seurat-helpers: Seurat Workflow Support

Link: baia-seurat-helpers

Provides utility functions that simplify common Seurat operations and serve as a foundation for many downstream analyses.

About BAIA

The BAIA Unit develops open-source software supporting:

Single-cell transcriptomics and Immune bioinformatics
Viral genomics and metagenomics
Malaria bioinformatics
AI-assisted qualitative research data analysis

GitHub Organization: github.com/baia-ipc