GDIS-Bio v1.1.0 — Expanded Reproducibility and Robustness Release

GDIS-Bio v1.1.0 — Expanded Reproducibility and Robustness Release

This release expands the reproducibility workflow accompanying:

“GDIS-Bio: A Generalized Dynamical Instability Framework for Localizing Transcriptional State Transitions in Single-Cell Trajectories”

Authors: Hamid Ismail, Ahmed Harb, Basem William, and Marwan Bikdash

GDIS-Bio v1.1.0 extends the original reproducibility release with additional reviewer-driven robustness analyses, alternative pseudotime and graph-geodesic ordering assessments, component-ablation analyses, improved pipeline validation, and expanded documentation.

Major additions

• Controlled GDIS component-ablation analysis.
• Pseudotime-order perturbation and robustness analyses.
• Alternative pseudotime reconstruction using diffusion pseudotime.
• Graph-geodesic reconstruction of developmental ordering.
• Cohort-wide geodesic reconstruction qualification.
• Alternative-ordering GDIS comparison and paired statistics.
• Additional supplementary figure and table generation.
• Dependence-aware coordinated-shift sensitivity analysis.
• Non-circular landmark null analysis.
• Pancreatic annotated-state IQR localization analysis.
• Fixed-cell-window pseudotime-span audit.
• Repository-level P25 validation utilities.
• Expanded reproducibility, provenance, reviewer-analysis, and release documentation.
• Improved README with installation, computational requirements, workflow organization, interpretation guidance, and citation information.

Datasets

The workflow analyzes two public single-cell RNA-seq datasets:

• GSE114412 — human pancreatic endocrine differentiation.
• GSE175634 — human iPSC-derived cardiac differentiation.

Reproducibility

The repository includes:

• sequential scientific analysis scripts;
• environment specifications;
• frozen analysis parameters;
• Linux and Windows execution helpers;
• P25 smoke and integrity validation;
• selected manuscript assets;
• documentation linking analyses to figures, tables, and reviewer-response stages.

Large raw and intermediate datasets are not bundled with the source release. They can be downloaded or regenerated using the supplied workflow.

Validation

The updated repository has been checked for:

• presence of all 44 primary analysis-stage scripts;
• Python syntax compilation;
• required P25 dependencies;
• repository cleanliness;
• P25 source-level smoke validation;
• compatibility with source-only GitHub checkout behavior.

Repository

https://github.com/hamiddi/GDIS-Bio

Version: v1.1.0
License: MIT