glue-genes 1.0

Multidimensional data visualization for genomics

The glue-genes meta-package

glue genes is a custom version of the glue software for the visual exploration of genomics data, developed in partnership with The Jackson Laboratory.

Features

glue genes provides all the core features of glue:

• Interactive, linked statistical graphics
• A user interface for 'glueing' together multiple datasets with complicated relationships
• A highly scriptable and extendable environment

In addition, glue genes provides:

• Data loaders for genomics data file formats such as .bed, .bigwig, .h5ad, and .loom
• Viewers including: 2D Heatmap, Small Multiples, QTL Viewer
• Menubar plug-ins to facilitate analysis of single-cell transcriptomics data

Install

Due to some complicated binary dependencies, the recommended procedure for installing this package is to use conda and install into a new environment as follows:

conda create -n glue-genes python==3.9
conda activate glue-genes

conda install glue-core
pip install glue-genes@git+https://github.com/gluesolutions/glue-genes.git

Usage

The Scanpy differential gene expression plugin requires some custom actions to run at startup, which can be achieved by starting glue using this command:

glue --startup=setup_anndata

Development

glue genes is currently under active development towards a 1.0 release. Please file all bug reports as github issues.