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Cholesteryl Ester Transfer Protein (CETP) as a Drug Target for Cardiovascular Disease

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posted on 30.07.2021, 11:18 by Floriaan SchmidtFloriaan Schmidt
Contains data and computer scripts to generate the figures underlying the manuscript: Cholesteryl Ester Transfer Protein (CETP) as a Drug Target for Cardiovascular Disease.

The README.md:
# Scripts and deposited data

This directory contains R and python scripts along with the data necessary to
generate the results described in the manuscript: 'cholesteryl ester transfer
protein (CETP) as a drug target for cardiovascular disease'.

## Directory content

.
├── README.md
├── scripts
├── figures
├── MR_data
├── TRIAL_data
└── PICKLED_data

The `scripts` directory contains the computer codes necessary to
generate the figures which get saved to the `figures` directory.

The scripts source data from the `MR_data` and `TRIAL_data` directories.
The `PICKLED_data` directory contains the python pickled files from
which we extracted the .csv files in `MR_data` -- these files can be ignored.

## Computer scripts

The directory root contains various R (.R) and python (.py) scripts that
will process the data files.

It also contains a `cetp_conda_env.yml` file to conda install the
necessary R and python modules:

```
cd scripts
conda env create -f cetp_conda_env.yml
```

This creates the `cetp` conda environment.

To generate the figures, please run the following `bash` script:

```
# run from the scripts directory
./run_scripts.sh
```

### Input and output

* scripts/MR_heatmap.py
: Takes the MR_data .tsv files and returns Figures 2 and 5.
* scripts/MR_metabolites.R
: Takes the MR_data .tsv/csv files and returns Figure 4.
* scripts/MR_forestplots.R
: Takes the MR_data .tsv files and returns Figure 3.
* scripts/RCT_forestplots.R
: Takes the TRIAL_data .xlsx files and returns Figure 1.


## Contact

Please contact Floriaan Schmidt for any queries: amand.schmidt@ucl.ac.uk .

Funding

BHF grant PG/18/5033837 and the UCL BHF Research Accelerator AA/18/6/34223

History

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I have considered whether the data to be published may be licensed commercially before deciding to freely release it to the public. Further information and advice may be sought from UCL Business https://www.uclb.com/about/our-people/

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