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README.md

Reprogram-Seq

Reprogram-Seq leverages organ-specific cell atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest.


 

Reprogram-Seq workflow

   

File organization

.
├── README.md
├── analyses
│   ├── cluster_10x_data.R
│   ├── cluster_drop-seq_data.R
│   ├── construct_trajectories.R
│   └── permute_pca_irlba.R
├── data
│   ├── 10x
│   │   ├── epicardial_10f_d7
│   │   │   └── tsne_out_coords.rds
│   │   ├── epicardial_3f_d7
│   │   │   ├── cell_dataset_lowerDetectionLimit0.5_DDRTree_dim2_reverse.rds
│   │   │   └── de_paired_primary_epicardial_uninfected.rds
│   │   ├── expr_readcount_raw_csc_dimnames.rds
│   │   ├── expr_readcount_raw_csc_indices_part1.rds
│   │   ├── expr_readcount_raw_csc_indices_part2.rds
│   │   ├── expr_readcount_raw_csc_indptr.rds
│   │   ├── expr_readcount_raw_csc_shape.rds
│   │   └── expr_readcount_raw_csc_values.rds
│   ├── drop-seq
│   │   ├── expr_readcount_raw_csc_dimnames.rds
│   │   ├── expr_readcount_raw_csc_indices.rds
│   │   ├── expr_readcount_raw_csc_indptr.rds
│   │   ├── expr_readcount_raw_csc_shape.rds
│   │   ├── expr_readcount_raw_csc_values.rds
│   │   └── tsne_out_coords.rds
│   └── misc
│       ├── genes.tsv
│       └── workflow.png
├── notebooks
│   ├── jupyter_notebooks
│   │   ├── conversion.ipynb
│   │   ├── embedding.ipynb
│   │   ├── embedding_fitsne.ipynb
│   │   └── embedding_umap.ipynb
│   └── rmarkdowns
│       ├── README.md
│       ├── global_reprogramming_of_transcription.html
│       ├── rational_epicardial_reprogramming.html
│       └── unbiased_reprogramming.html
└── pipelines
    ├── 10x.sh
    └── drop-seq.sh

 

Notebooks

Jupyter notebooks (in development)

Conversion of R objects to Python objects
Exploration of recent advances in single cell visualization
        UMAP
        Fl-tSNE
...

HTML documents created from R Markdown (to recreate figures)

Unbiased reprogramming (4.3 Mb)
Rational epicardial reprogramming (2.9 Mb)
Global reprogramming of transcription (5.0 Mb)  

How to cite

Rational reprogramming of cellular states by combinatorial perturbation
Jialei Duan, Boxun Li, Minoti Bhakta, Shiqi Xie, Pei Zhou, Nikhil V. Munshi, Gary C. Hon
doi: https://doi.org/10.1101/468249

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