Single-cell perturbation analysis
python bioinformatics computational-biology drug-discovery scrna-seq crispr single-cell differential-expression perturbation anndata scverse differential-abundance perturb-seq
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Sep 7, 2026 - Python
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perturb-seq
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Single cell Perturbations - Analysis of Differential gene Expression
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Feb 10, 2025 - Python
Recovering gene regulatory networks from Perturb-seq by fitting steady-state ODEs through frozen single-cell foundation models (GenBio @ ICML 2026)
stack ode crispr single-cell interpretability tahoe grn gene-regulatory-network scprint foundation-models perturb-seq scgpt single-cell-foundation-model
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Jun 23, 2026 - Python
Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation
bioinformatics rna-seq time-series systems-biology scrna-seq crispr immunology atac-seq transcriptomics epigenomics perturbations systems-immunology crop-seq perturb-seq
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Jul 20, 2025 - Jupyter Notebook
Epigenetic regulators of fibrotic transformation in cardiac fibroblasts
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Jan 14, 2026 - Jupyter Notebook
Agentic gene perturbation prediction system for the MLGenX BioReasoning Challenge – Track B.
bioinformatics computational-biology gene-perturbation rag langchain perturb-seq langgraph agentic-ai mlgenx
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Jul 23, 2026 - Jupyter Notebook
A single-cell RNAseq pipeline for perturb-seq data
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Feb 21, 2024 - WDL
Reproducible computational vignettes for the CRISPR-perturbation multi-omics identifiability review (Asediya, Briefings in Bioinformatics)
crispr reproducibility causal-inference functional-genomics multi-omics perturb-seq livestock-genomics
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Jun 30, 2026 - Python
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.
bioinformatics rna-seq snakemake ngs bioinformatics-pipeline scrna-seq crispr single-cell bioinformatics-analysis single-cell-rna-seq perturbation ngs-pipeline fair-principles perturb-seq
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Dec 21, 2025 - Jupyter Notebook
Analysis code for Perturb-ME: scalable mechanism discovery from phenotype-enriched genome-wide CRISPR screens (Wang, Gu, Frangieh et al., bioRxiv 2026)
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Aug 18, 2026 - Python
Runnable Perturb-seq analysis pipeline (guide assignment, Mixscape, pseudobulk-vs-per-cell DE, E-distance) on the Papalexi 2021 ECCITE-seq CRISPR screen — pertpy + scanpy
bioinformatics computational-biology single-cell differential-expression scanpy crispr-screen perturb-seq pertpy
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Jun 19, 2026 - Python
A hands-on virtual cell perturbation prediction course for experimental biologists.
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Jul 13, 2026 - Jupyter Notebook
Fast exact short-DNA known-target assignment for CRISPR guides, barcodes, primers, panels, and whitelists.
python c bioinformatics genomics sequencing computational-biology edit-distance bioconda crispr fastq sequence-analysis feature-barcodes crispr-screen perturb-seq barcode-demultiplexing guide-counting guide-capture short-dna
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Sep 7, 2026 - Python
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.
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Jan 7, 2026 - R
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.
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Jun 14, 2026 - Python
Perturbation Prediction Model for the Kaggle Challenge: "Myllia| Echoes of Silenced Genes: A Cell Challenge"
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Mar 13, 2026 - Jupyter Notebook
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.
benchmark bioinformatics statistics mcp computational-biology meta-analysis reproducibility single-cell llm-agents perturb-seq model-context-protocol
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Jul 16, 2026 - HTML
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