razofz / db_qz_multiome

Multiome (RNA+ATAC from same cell) data generated by Qinyu Zhang in David Bryder's lab. Paper here: https://doi.org/10.7554/eLife.91826.2

DB_QZ-multiome

Accompanying code for Ex vivo Expansion Potential of Murine Hematopoietic Stem Cells: A Rare Property Only Partially Predicted by Phenotype, published in eLife. https://doi.org/10.7554/eLife.91826.2

Multiome data generated by Qinyu Zhang in David Bryder's lab.

The code used in the manuscript resides in the notebooks directory.

Project Organization

├── LICENSE
├── multiome.smk
├── multiome-config.yaml
├── README.md          <- The top-level README for developers using this project.
├── data
│   ├── external       <- Data from third party sources.
│   ├── interim        <- Intermediate data that has been transformed.
│   ├── processed      <- The final, canonical data sets for modeling.
│   └── raw            <- The original, immutable data dump.
│
├── docs               <- A default Sphinx project; see sphinx-doc.org for details
│
├── notebooks          <- Jupyter notebooks.
│
├── references         <- Data dictionaries, manuals, and all other explanatory materials.
│
├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc.
│   └── figures        <- Generated graphics and figures to be used in reporting
│   └── snakemake      <- Snakemake report output (html report, graphs etc)
│
├── envs               <- YAML files specifying the conda environments used in the project.
│
└── src                <- Source code for use in this project.
    └── snakemake

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Project based on the cookiecutter data science project template. #cookiecutterdatascience