reproducibility_ws_imputation
Science Score: 44.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Scientific vocabulary similarity
Low similarity (10.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: PMerbaum
- License: mit
- Language: Python
- Default Branch: main
- Size: 17.6 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
repeat_imputation
This project is a part of short tandem repeat (STR) imputation accuracy analysis. Allele lengths are cruisial in some cases. For example, for patients with amyotrophic lateral sclerosis - a C9ortf72 gene that has longer than 30 STR's means shorter survival and more aggressive disease. Therefore, it is crucial to be able to predict (impute) the length of C9ORF72 gene in all samples. We established a method to calculate these lengths for SNP array data. We tested our model with known repeat lengths calculated with ExpansionHunter - we masked C9ortf72 gene region, reimputed it and now we check, how accurate our imputation is with buildrocimputation_accuracy.py.
Usage
Upload the buildrocimputation_accuracy.py function and simulated data from data/raw folder. Data is formated as a dataframe and contains name of samples, phased imputed lengths that were extracted from imputed.vcf file, phased true lengths extracted from ExpansionHunter.vcf file and a dosage calulated during the imputation with Beagle software.
Project Structure
The project structure distinguishes three kinds of folders: - read-only (RO): not edited by either code or researcher - human-writeable (HW): edited by the researcher only. - project-generated (PG): folders generated when running the code; these folders can be deleted or emptied and will be completely reconstituted as the project is run.
``` . ├── .gitignore ├── LICENSE ├── README.md ├── requirements.txt ├── data <- All project data, ignored by git │ ├── raw <- The original, immutable data dump. (RO) ├── docs <- Documentation notebook for users (HW) │ ├── manuscript <- Manuscript source, e.g., LaTeX, Markdown, etc. (HW) │ └── reports <- Other project reports and notebooks (e.g. Jupyter, .Rmd) (HW) ├── results │ ├── figures <- Figures for the manuscript or reports (PG) │ └── output <- Other output for the manuscript or reports (PG) └── src <- Source code for this project (HW)
```
Add a citation file
Create a citation file for your repository using cffinit
License
This project is licensed under the terms of the MIT License.
Owner
- Login: PMerbaum
- Kind: user
- Repositories: 1
- Profile: https://github.com/PMerbaum
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "My Research Software"
authors:
- family-names: Druskat
given-names: Stephan
orcid: https://orcid.org/1234-5678-9101-1121
version: 2.0.4
date-released: 2021-08-11
doi: 10.5281/zenodo.1234
license: Apache-2.0
repository-code: "https://github.com/citation-file-format/my-research-software"