signeRFlow is a shiny app that allows users to explore mutational signatures and exposures to related mutational processes embedded into signeR package. With the available modules, users are able to perform analysis on their own data by applying different approaches, such as de novo and fitting. Also, there is a module to explore public datasets from TCGA.
In order to use signeRFlow app, you must have signeR package installed. To install signeR, open R and enter:
There are three available modules in the app:
You can go through the modules independently by using the app sidebar.
In this module, you can upload an SNV matrix with counts of mutations and execute the signeR de novo algorithm, which computes a Bayesian approach to the non-negative factorization (NMF) of the mutation counts in a matrix product of mutational signatures and exposures to mutational processes.
You can also provide a file with opportunities that are used as weights for the factorization. Further analysis parameters can be set, results can be visualized on different plots and found signatures can be compared to the ones in Cosmic data