Data

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Open Source Science

https://github.com/biocomputingup/cagi-p16-assessment

https://genomeinterpretation.org/content/predict-how-variants-p16-tumor-suppressor-protein-affect-cell-proliferation

https://github.com/biocomputingup/cagi-p16-assessment

Science Score: 13.0%

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    Low similarity (7.2%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

https://genomeinterpretation.org/content/predict-how-variants-p16-tumor-suppressor-protein-affect-cell-proliferation

Basic Info
  • Host: GitHub
  • Owner: BioComputingUP
  • Language: R
  • Default Branch: master
  • Size: 25.4 KB
Statistics
  • Stars: 0
  • Watchers: 5
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 9 years ago · Last pushed about 9 years ago
Metadata Files
Readme

README.md

CAGI-p16-assessment

Overview

This repository contains all the R scrips used for the assessment of the CAGI-3 "p16 challenge".

All the scripts can be reused for performance assessment of bioinformatics tools to predict phenotypic effects of genetic variants of unknown significance (VUS).

Dependencies

The analysis requires the following R packages to be installed

Usage

Each script can be run from a terminal as the example below

Rscript 1_main_numerical_assessment.R

Details

In this section a brief description of each script is given

Script | Description ------------ | ------------- 1 | calculates the main numerical measures (i.e. correlations, AUC, RMSD).In additions it produces the tables needed by other scripts to generate assessment figures and tables. 2 | calculates correlation measure among all predictions and produce an heatmap figure to visualize results 3 | calculates correlation measure among performance indices and produce an heatmap figure to visualize results 4 | calculates the pairwise significance of challenge evaluations and produce an heatmap figure 5 | draws experimental values versus predicted values graph 6 | calculates only PSWD10 and produce a table to identify difficut targets

Owner

  • Name: BioComputing Group, University of Padova
  • Login: BioComputingUP
  • Kind: organization
  • Email: biocomp@bio.unipd.it
  • Location: Italy

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marcocarraro c****9@g****m 9
Francesco Tabaro f****o@g****m 2

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