Analysis of protoemics data from this paper: https://doi.org/10.1038/nbt.3418
- Python 3
- R
- Git (or any Git client of your choice, e.g. Github Desktop)
this should in the future be running a docker container
- install docker if not already done
- navigate to this file in the console and run:
docker-compose run --service-ports notebook- after building a command prompt should open allowing you to open jupyter-notebooks
- to open a jupyter notebook run
jupyter-notebook --allow-root|- data science
| |- code/ # all programmatic code relating to the project
| | +- templates/ # scripts for generating template files
| |
| |- data/ # all data from the study
| | |- raw_internal/ # raw data generated in-lab or by collaborators, will not be altered
| | |- raw_external/ # data from third-party sources, databases etc, will not be altered
| | |- intermediate/ # intermediate data on its way from raw to final
| | +- final/ # final data for figures/visualizations
| |
| |- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- doc/ # documentation for the study and other explanatory material
|
|
|- .env # file to store passwords and usernames needed for the scripts. This
| will not get synced to GitHub.
|- .gitignore # files that will not sync to Github
|- LICENSE # license
|- README.md # the top level description of content
|- requirements.txt # the requirements file for reproducing the analysis environment,
| e.g. generated with `pip freeze > requirements.txt`
+- to-dos.md # pending things that are yet to be done
Navigate to each folder's README.md to learn more about the corresponding section.
The initial file and directory structure of this project was developed by a group of participants in the Reproducible Science Curriculum Workshop, held at NESCent in December 2014. The structure is based on, and heavily follows the one proposed by Noble 2009, with a few but small modifications. The original repository has been modified by Martin Engqvist and the one presented here differs in some ways. Additional modifictations have been added by Jonas Sindlinger.