Single cell Perturbations - Analysis of Differential gene Expression

The python software to run mpeg framework.

Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation

Recovering gene regulatory networks from Perturb-seq by fitting steady-state ODEs through frozen single-cell foundation models (GenBio @ ICML 2026)

Epigenetic regulators of fibrotic transformation in cardiac fibroblasts

A reproducible computational pipeline for processing and analyzing single-cell RNA-seq data with CRISPR perturbations (Perturb-seq), designed for the Virtual Cell Challenge 2025. Features automated quality control, normalization, class balancing, and batch integration using Snakemake.

A single-cell RNAseq pipeline for perturb-seq data

Reproducible computational vignettes for the CRISPR-perturbation multi-omics identifiability review (Asediya, Briefings in Bioinformatics)

Agentic gene perturbation prediction system for the MLGenX BioReasoning Challenge – Track B.

Ask a meta-analysis in plain English and it tells you whether the statistics support one combined number, refusing when they do not. Every number is computed by a tested toolkit, never the model. Also a Model Context Protocol server.

Perturbation Prediction Model for the Kaggle Challenge: "Myllia| Echoes of Silenced Genes: A Cell Challenge"

JCAP CRISPR Mixscape Pipeline is a user-friendly R Shiny application for interactive single-cell CRISPR screen analysis. It enables rapid quality control, visualization, and differential expression discovery using Mixscape and Seurat, all in a point-and-click environment. Ideal for researchers working with Perturb-seq data.

Reproducible conditional-risk, crossover and selection-regret analyses for response-regime-aware evaluation of single-cell perturbation predictors.

Null-Stratified Rank Accuracy (NSRA): a rank-based metric for evaluating Perturb-seq predictions.

Rigorous benchmark of single-cell CRISPR perturbation x condition response prediction (melanoma Perturb-CITE-seq): effect-level (delta) metrics, random forest vs linear vs CPA.

Analysis scripts of IGVF ESC engineering project.

PertPy-based perturbation analysis pipeline using a CRISPR Perturb-seq dataset with reproducible Python scripts.

A hands-on virtual cell perturbation prediction course for experimental biologists.

Wayfinder — a hypothesis referee that says a confident no: receipt-backed literature-based discovery, tested against CD4+ T-cell Perturb-seq data and built in Claude Science. (Built with Claude: Life Sciences)