https://github.com/immunogenomics/craft-seq
Code for analysis of CRAFT-seq data
https://github.com/immunogenomics/craft-seq
Last synced: about 1 month ago
JSON representation
Code for analysis of CRAFT-seq data
- Host: GitHub
- URL: https://github.com/immunogenomics/craft-seq
- Owner: immunogenomics
- Created: 2024-03-27T18:14:52.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2025-05-15T16:08:30.000Z (about 1 year ago)
- Last Synced: 2025-06-27T18:43:56.435Z (about 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 54.6 MB
- Stars: 1
- Watchers: 11
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# CRAFTseq
This repo provides code for the analysis of CRAFTseq data corresponding to [Baglaenko, et al, biorxiv, 2024](https://www.biorxiv.org/content/10.1101/2024.03.28.587175v1).
Contact: [Yuriy Baglaenko](yuriy.baglaenko@cchmc.org), [Zepeng "Phoenix" Mu](zemu@bwh.harvard.edu)
[](https://doi.org/10.5281/zenodo.15425509)
Contained in this repo are notebooks or scripts for the analyses and figures included in the manuscript. We have also provided a [tutorial](./example/Example_CraftSeq.ipynb) notebook for the entire pipeline of analyzing data produced by CRAFTSeq. This notebook utilizes data produced from the PTPRC experiment.
| Experiment | Figure # | Notebooks/Scripts | Notes |
|--------|----------|----------|----------|
| PTEN | Figure 1 | [PTEN Notebook.ipynb](./figures/PTEN/PTEN_FBXO11_DQB1_Github.ipynb) | Joint Notebook with DQB1/FBXO11. No CRISPR editing |
| FBXO11 | Figure 2 | [FBXO11_Run 1 Notebook.ipynb](./figures/FBXO11/PTEN_FBXO11_DQB1_Github.ipynb)
[FBXO11_Run 2 - Joint Analysis.ipynb](./figures/FBXO11/FBXO11_Run2_Joint_Github.ipynb)| Run 1 and Run 2 merged and analyzed together. Alternative splicing to induce a knockout with CRISPR |
| DQB1 | Figure 2 | [DQB1_Notebook.ipynb](./figures/DQB1/PTEN_FBXO11_DQB1_Github.ipynb)
[DQB1_Heatmap.ipynb](./figures/DQB1/DQB1_Heatmap_Github.ipynb)| CRISPR-Cas cutting and HDR in HLA-DQB1. |
| PTPRC | Figure 3 | [PTPRC_Notebook.ipynb](./figures/PTPRC/PTPRC_Github.ipynb)
[GSEA_PTPRC_IL2RA.ipynb](./figures/Misc/GSEA_PTPRC_IL2RA.ipynb)
[Bootstrapping CD45 Data.ipynb](./figures/PTPRC/PTPRC_Analysis_Bootstrap_Laters.ipynb)| Induction of ESC with CRISPR base editors|
| RPL8 | Figure 4 | [RPL8_Notebook.ipynb](./figures/RPL8/RPL8_Github.ipynb)| RPL8 eQTL CRISPR base editing |
| IL2RA | Figure 4 | [IL2RA_Run 1.ipynb](./figures/IL2RA/IL2RA_Run1_Github.ipynb)
[IL2RA_Run 2.ipynb](./figures/IL2RA/IL2RA_Run2_Github.ipynb)
[IL2RA_Joint Analysis Notebook 2.ipynb](./figures/IL2RA/IL2RA_joint_Github.ipynb)
[GSEA_PTPRC_IL2RA.ipynb](./figures/Misc/GSEA_PTPRC_IL2RA.ipynb)| CRISPR editing of IL2RA variant in Th1 and Treg polarized naive CD4 T cells
| PAX5 | Figure 5 | [PAX5_genotype_analysis.R](./figures/PAX5/PAX5_genotype_analysis.R)
[PAX5_RNA_analysis.R](./figures/PAX5/PAX5_RNA_analysis.R)
[PAX5_RNA_glmNB.R](./figures/PAX5/PAX5_RNA_glmNB.R)
[PAX5_ADT_glmNB.R](./figures/PAX5/PAX5_ADT_glmNB.R)
[PAX5_genotyping.ipynb](./figures/PAX5/PAX5_AlleleCalling_Github.ipynb)| PAX5 multiplexed editing with CRIPSR base editors |
| Misc | | [Mixscape_Comparison_Latest.ipynb](./figures/Misc/Mixscape_Comparison_Latest.ipynb)
[TotalAlignmentStats_Latest.ipynb](./figures/Misc/TotalAlignmentStats_Latest.ipynb)
[Example Flow Cytometry Analysis.ipynb](./figures/Misc/PTEN_FBXO11_DQB1_Flow_Github.ipynb) | Extras |
| Supplemental Note | |[Supplemental Note and Genotype Calling.ipynb](./figures/SupplementaryNote/SupplementaryNote_Github.ipynb) | Fully replicatable genotyping analysis. Key files deposited in folder |
File: [DNA Filtering Functions](./figures/DNA_filtering_Functions.R) has updated function on allele calling and genotyping of single cell along with extra utility functions.
Sample data for the PTEN, FBXO11, and DQB1 experiments is located on [Zenodo](https://zenodo.org/records/10932681). GEO records are being generated to deposit count matrices with trimmed meta data, and dbGAP records will be made available for raw sequencing data. QCed data from the PTPRC experiment is also available on [Zenodo](https://zenodo.org/records/15114923) and utilized in our [tutorial](./example/Example_CraftSeq.ipynb) notebook.