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🪱 Cellular Drivers of Divergent Reproductive Fates in P. morgani

This repository contains the analysis notebook, results, and presentation slides from a study on the cellular mechanisms underlying reproductive fate decisions in the freshwater planarian Phagocata morgani.

The project report can be viewed at 🔗https://aishwarya-girish.github.io/Dorrity-Lab-EMBL-Internship/.

🪱 Overview

Developmental bifurcations represent critical transitions where organisms diverge into distinct phenotypic fates. In P. morgani, individuals develop into either a sexual or asexual reproductive phenotype—each associated with a distinct growth trajectory. The specific cellular populations that guide this bifurcation remain poorly characterized.

This repository presents a quantitative framework to:

  • Infer trajectories using pseudotime
  • Identify bifurcation points along these trajectories
  • Model cell-type abundance and variance changes across transitions
  • Statistically detect cell types enriched near bifurcation points that may drive reproductive fate
  • Model size-independent covariance in the cell types

📂 Repository Structure

Main Files
├── Dorrity_Lab_EMBL.Rmd # Main analysis notebook
├── size-cds-cellcounts_3e-5-highRes-cell-type.rds # Input data
├── Work_Presentation.pptx # Summary presentation of the study

Output Directories
├── trajectory_output/ 
├── abundance_output/
├── variance_output/
├── combined_analysis_output/
├── covariance_output/

Extras
├── bifurcation.jpeg # Illustration for README
├── worm.jpeg # Illustration used in index.html
├── index.html # Rendered notebook output
└── README.md # Project overview and instructions

📎 Requirements

All analyses are performed within an RNotebook framework using R (version 4.4.2). The Monocle3 package (Trapnell lab) is utilized for single-cell trajectory inference and normalization. Dependencies including Bioconductor packages and common data manipulation and visualization libraries are mentioned in the RNotebook "Dorrity_Lab_Embl.Rmd".

🪱 How to Run the Analysis

To reproduce the full analysis:

  1. Clone this repository: 
    git clone https://github.com/Aishwarya-Girish/Dorrity-Lab-EMBL-Internship.git
cd Dorrity-Lab-EMBL
  2. Open planarian_reproductive_fate_drivers.Rmd in RStudio.
  3. Run the notebook or run chunks interactively to reproduce results.

🪱 Academia Bifurcations: This is not a UMAP, it's a career path 😁

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