asthma_bal

explore association between nasal/bronchial gene expression and serum/BAL eosinophil counts

Project Organization

├── CITATION.cff <- Contains metadata on how the project might eventually be published. ├── LICENSE ├── DEGrawoutput <- contains raw DEG results that are excluded from git respository ├── Makefile <- Makefile with commands like make data or make train ├── README.md <- The top-level README for developers using this project. ├── config <- Configuration options for the analysis. | ├── config.yaml <- Snakemake config file. | └── samples.tsv <- A metadata table for all the samples run in the analysis.
│ ├── docs <- A default Sphinx project; see sphinx-doc.org for details │ ├── environment.yaml <- The requirements file for reproducing the analysis environment, e.g. │ generated with conda env export > environment.yaml │ ├── img <- A place to store images associated with the project/pipeline, e.g. a │ a figure of the pipeline DAG. │ ├── notebooks <- Jupyter or Rmd notebooks. Naming convention is a number (for ordering), │ the creator's initials, and a short - delimited description, e.g. │ 1.0-jqp-initial-data-exploration. │ ├── 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 │ ├── resources <- Place for data. By default excluded from the git repository. │ ├── external <- Data from third party sources. │ ├── processeddata <- Processed data used for further analysis. │ ├── workingdata <- copy of raw data used for work. │ └── rawdata <- The original, immutable data dump. │ ├── results <- Final output of the data processing pipeline. By default excluded from the git repository. │ ├── sandbox <- A place to test scripts and ideas. By default excluded from the git repository. │ ├── scripts <- A place for short shell or python scripts. │ ├── setup.py <- Makes project pip installable (pip install -e .) so src can be importe │ ├── src <- Source code for use in this project. │ ├── _init__.py <- Makes src a Python module ├── tox.ini <- tox file with settings for running tox; see tox.readthedocs.io │ ├── workflow <- Place to store the main pipeline for rerunning all the analysis. │ ├── envs <- Contains different conda environments in .yaml format for running the pipeline. │ ├── rules <- Contains .smk files that are included by the main Snakefile, including common.smk for functions. │ ├── scripts <- Contains different R or python scripts used by the script: directive in Snakemake. │ ├── Snakefile <- Contains the main entrypoint to the pipeline. │ ├── workspace <- Space for intermediate results in the pipeline. By default excluded from the git repository.

Project inspired by the cookiecutter data science project template and the Snakemake workflow template.