Single cell Perturbations - Analysis of Differential gene Expression
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Feb 10, 2025 - Python
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perturb-seq
Here are 9 public repositories matching this topic...
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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Sep 29, 2025 - Jupyter Notebook
A single-cell RNAseq pipeline for perturb-seq data
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Feb 21, 2024 - WDL
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 scripts of IGVF ESC engineering project.
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Nov 14, 2024 - Jupyter Notebook
Interpretable perturb-seq modeling with a pathway/TF concept bottleneck — predicts effects and identifies stable regulatory drivers that generalize across datasets.
bioinformatics reproducible-research systems-biology single-cell pathway-analysis causal-inference interpretable-ml perturb-seq concept-bottleneck
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Oct 15, 2025 - 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
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