markeR

markeR provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data.

Key Features:

• Quantitative and visual analyses: Supports both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes.
• Multiple evaluation methods: Implements score-based and enrichment approaches for gene set evaluation.
• Individual gene exploration: Allows the exploration of expression behaviour of individual genes.
• Gene set similarity assessment: Enables assessment of the similarity of user gene sets against established collections such as MSigDB.

Scientific Applications:

• Phenotypic marker evaluation: Evaluates gene sets as phenotypic markers using transcriptomic data.
• Biological interpretation: Facilitates biological interpretation by comparing gene sets against established collections.

Methodology:

Implements score-based and enrichment approaches for gene set evaluation.