Myeloproliferative neoplasm patient cohort data visualization

This web application allows the user to explore interactively data from a cohort of 113 myeloproliferative neoplasm (MPN) blood donors and 15 healthy blood controls.
To ensure that the dependencies are fulfilled, you can install the packages needed by running the install_dependencies.R script:

Rscript install_dependencies.R

Features

Cohort exploration

Represent and compare graphically several variables describing the cohort.

Variants exploration

Filter variants to select only the somatic mutations with sufficient evidence. Represent mutated gene per patient and co-occurrence of variants, as well as variants per disease and disease subtypes.

Aberrations and gene fusions exploration

Represent co-occurences of variants and genomic aberrations, occurences of aberrations per disease.
Display summary of genetic events per patient and per disease.
A network, sketching the co-occurences identified for aberrations, mutations and diseases in the other tabs, is also available.

Changelog

v0.1

Implement basic cohort description plots

v0.2

Implement basic variants description plots

v0.3

Implement full CSS layout

v0.4

Implement aberration description plots, and patient-wise Circos plots.

v0.5

Implement disease-wise Circos plots.

v0.6

Implement co-occurence networks.

To-do list

Cohort exploration

• Take into account NAs, non relevant-points and redundancy
• Sort legend on pie charts

Variants exploration

• Correct color scheme of one by one matrices

Gene expression exploration

Differential splicing antigen summary

Interface and texts

• Complete introduction text