HTSanalyzeR

HTSanalyzeR performs integrative analysis of high-throughput screening (HTS) data to identify enriched and over-represented gene sets, compare gene set responses between conditions, and detect rich subnetworks from RNA interference (RNAi) and small-molecule perturbation experiments.

Key Features:

• Integrated Analysis Pipelines: Provides customizable pipelines that support over-representation analysis, gene set enrichment analysis (GSEA), comparative gene set analysis, and identification of rich subnetworks.
• Interoperability with Pre-processing Tools: Interfaces with commonly used pre-processing packages for HTS data, enabling analysis starting from prepared inputs such as cellHTS2 objects.

Scientific Applications:

• Gene Set Over-representation and Enrichment Analysis: Identifies significantly over-represented gene sets and performs GSEA to reveal biological processes affected by perturbations.
• Comparative Gene Set Analysis: Compares gene set-level responses across datasets or experimental conditions to detect differential pathway activation.
• Network Analyses: Detects rich subnetworks and integrates network-level insights, including analyses on cellHTS2 objects for RNAi screens.

Methodology:

Implements over-representation analysis, gene set enrichment analysis (GSEA), comparative gene set analysis, and identification of rich subnetworks.