Multidimensional data visualization for genomics
Project description
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.
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