psichomics

psichomics quantifies alternative splicing and performs integrative analyses of alternative splicing and gene expression from TCGA, GTEx, SRA, and user-provided RNA-seq data.

Key Features:

• Alternative Splicing Quantification: Quantifies alternative splicing using exon-exon junction information from RNA-seq data.
• Differential Splicing Analysis: Performs median- and variance-based differential splicing analyses.
• Differential Gene Expression Analysis: Performs median- and variance-based differential gene expression analyses.
• Survival Analysis: Performs survival analyses incorporating clinical and molecular sample-associated features.
• Dimensionality Reduction: Performs dimensionality reduction analyses on alternative splicing and gene expression data.
• Integrative Analysis with Clinical Features: Incorporates clinical and molecular sample-associated features such as tumour stage or survival into downstream analyses.
• Genomic Mapping and Functional Annotation: Provides visual access to genomic mapping and functional annotation of selected alternative splicing events.

Scientific Applications:

• Cancer Research: Identifies alternative splicing signatures specific to cancer stages and novel putative prognostic factors, as demonstrated in stage I breast cancer.
• Pathology Studies: Investigates dysregulation of alternative pre-mRNA splicing associated with various pathologies.
• Physiological Context Analysis: Enables global studies of alternative splicing in different physiological and disease contexts using next-generation sequencing data.

Methodology:

psichomics is implemented as an R package with a Shiny-based graphical interface. The tool processes data from TCGA, GTEx, SRA, and user-provided sources, performing integrative analyses that combine alternative splicing quantification with gene expression, survival, dimensionality reduction, and differential analyses while incorporating clinical and molecular sample-associated features.