psichomics

psichomics performs quantification and analysis of alternative splicing from RNA sequencing datasets and integrates TCGA, GTEx, and clinical metadata to support differential splicing, survival analysis, and exploratory analyses such as principal components analysis (PCA).

Key Features:

• Quantification of alternative splicing: Quantifies alternative splicing events from RNA sequencing-derived datasets.
• Differential splicing analysis: Performs statistical analysis to identify differential splicing between sample groups.
• Survival analysis: Relates splicing events to patient survival using survival analysis methods.
• Principal components analysis (PCA): Provides PCA for exploratory analysis of splicing variation.
• Integration with TCGA and GTEx: Imports and integrates splicing and expression data from TCGA and GTEx projects.
• Clinical metadata integration: Incorporates clinical features such as tumor stage and patient survival into analyses.
• Visualization of splicing data: Generates visualizations of alternative splicing events and analysis results.
• Bioconductor interoperability: Interoperates with Bioconductor packages for R-based genomic analyses.

Scientific Applications:

• Cancer genomics: Characterizes alternative splicing events in cancer and identifies events potentially relevant to tumor biology and therapeutic targeting.
• Prognostic biomarker discovery: Associates splicing events with patient survival and clinical parameters to support biomarker identification.
• Cross-tissue splicing analysis: Compares splicing patterns across tissues using GTEx and TCGA RNA-seq data.
• General RNA-seq splicing studies: Enables detailed analysis of alternative splicing in non-oncology RNA sequencing studies.

Methodology:

Integration with Bioconductor for R-based genomic data handling and application of statistical methods for quantification, differential splicing analysis, PCA, and survival analysis.