Guide

Guide performs analysis of RNA-Seq and microarray gene expression data for differential expression and pathway-level interpretation using R and Bioconductor.

Key Features:

• Differential Expression Analysis: Performs gene-centric differential expression analysis at both the gene and pathway levels for RNA-Seq and microarray datasets.
• Pathway Analysis: Implements pathway-level analysis using R/Bioconductor packages, including limma.
• Data Integration: Integrates gene annotation data and orthologue information to enrich biological interpretation.
• R Command Customization: Allows direct editing of underlying R commands to modify or extend analyses.
• Results Presentation: Produces figures and interactive tables for visualization and result exploration.

Scientific Applications:

• Gene Expression Analysis: Analysis and interpretation of RNA-Seq and microarray gene expression datasets.
• Differential and Pathway-Level Interpretation: Identification of differentially expressed genes and pathway-level changes using Bioconductor methods.
• Annotation-Enriched Interpretation: Use of gene annotation and orthologue information to provide additional contextual annotation of results.
• Custom Analyses in R: Extension and customization of analyses via direct modification of R commands.

Methodology:

Integration with R and Bioconductor modules; differential expression analysis at gene and pathway levels; pathway analysis using limma; incorporation of gene annotation and orthologue information; direct execution/editing of R commands; generation of figures and interactive tables.