a web-based application for integrative analysis
of copy number alterations
Launch Tool

Integrative analysis of copy number alterations

CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features.

Re-Seg & Score

Region profile

Classifier model

CNApp sections

Re-Seg & Score

Re-segmentation, CNA Scores computation and variable association

Sample CNA profiling, CNA levels quantification, statistical tests for variable associations

Region profile

Genome region profiling

CNA region profiles, CNA region frequencies, correlation profiles and descriptive regions

Classifier model

Machine-learning classification model predictions

Assessment of the classificatory potential from multiple variables (by randomForest)

About CNApp

CNApp has been developed using Shiny R package (version 1.1.0), from R-Studio, and code is freely available at GitHub.


CNApp can also be downloaded and installed as local tool by following instructions specified in the README file, in the GitHub account.

Please, cite our paper - in eLife journal - where we present CNApp tool:

CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications Sebastia Franch-Exposito, Laia Bassaganyas, Maria Vila-Casadesus, Eva Hernandez-Illan, Roger Esteban-Fabro, Marcos Diaz-Gay, Juan Jose Lozano, Antoni Castells, Josep M. Llovet, Sergi Castellvi-Bel, Jordi Camps; eLife 2020;9:e50267; doi: 10.7554/eLife.50267

Developed by CNApp team

Sebastià Franch Expósito, Ph.D.

  ORCID logo
Memorial Sloan Kettering Cancer Center - Research Fellow

Laia Bassaganyas, Ph.D.

  ORCID logo
University of Cambridge - Research Associate

Jordi Camps, Ph.D.

ORCID logo
IDIBAPS group leader - Associate Professor
at Universitat Autònoma de Barcelona

Institutions involved:

Sponsored by: