v1.0

gGnome v1.0

We are happy to announce the release of gGnome v1.0

The release of this version includes many bug fixes as well as the introduction of some new functionalities as compared to the original introduction of gGnome in the Hadi et al. 2020 paper. In these release notes we outline some of the changes.

Balance

balance is a function for inferring segment and junction copy number using the junction-balance paradigm through mixed-integer programming (see Hadi et al. for more details). It takes as input a gGraph with segment copy number estimates stored in the node metadata and applies junction balance to infer integer node and segment copy numbers. To run balance, users will need to install CPLEX. balance is the core function used by JaBbA. More details are available in the tutorial.

Versioning

With this release we introduce versioning for the first time for gGnome. Going forward, we plan to occasionally release minor versions (e.g. v1.1, v1.2) that include minor enhancements and bug fixes that should not fundamentally change the way gGnome works. When we make significant changes that either significantly modify a major functionality or introduce a new major feature then we will release a major version (e.g. v2.0).

CPLEX installation

Installing the CPLEX optimizer is not necessary to use the vast majority of gGnome’s functions. However, gGnome includes four functions (balance, fitcn, maxflow, and peel) that involve mixed integer programming and require CPLEX. Researchers can obtain a free academic license to use this software.

Streamline interactive visualization with gGnome.js

This version includes the new function gGnome.js() that allows you to easily process your gGraphs and coverage depth to visualize with the gGnome.js interface. The detailed usage description of this function is outlined in the tutorial. Briefly, gGnome.js() accepts a table that includes the paths to coverage and gGraphs (RDS files) for each sample in a dataset and processes these files to generates a folder containing all files necessary for gGnome.js usage.

Many bug fixes

We have made a major effort to get the package to be as stable as possible by fixing bugs that we found. But if you run into any issues, please report your issues on github.