classifieRc

classifieRc performs transcriptional subtype classification and functional annotation of colorectal cancer (CRC) transcriptomes to support molecular subtyping and biological interpretation.

Key Features:

• Subtype Classification: Assigns CRC samples to established molecular subtype frameworks including the four Consensus Molecular Subtypes (CMS) and five intrinsic CRIS subtypes (CRIS).
• Cross-Platform Compatibility: Processes transcriptional data from diverse assay and sequencing platforms for unified subtype assignment.
• Cellular Composition Estimation: Estimates sample cell-type composition using MCP-counter and xCell.
• Gene Set Enrichment Analysis (ssGSEA): Performs single-sample GSEA (ssGSEA) to profile pathway and gene-set activity per sample.
• Transcription Factor Activity Prediction: Predicts transcription factor activities using DoRothEA.

Scientific Applications:

• Molecular Subtyping of CRC: Classifies colorectal cancer samples into CMS and CRIS subtypes to enable subtype-specific analyses.
• Prognostic and Therapeutic Insight: Generates subtype and pathway-level annotations that can inform prognosis and potential treatment strategies.
• Discovery Research: Supports investigation of regulatory mechanisms, cellular composition, and pathway activity in transcriptome datasets.

Methodology:

Assigns samples to CMS and CRIS subtypes using established classifier gene sets and applies MCP-counter, xCell, ssGSEA, and DoRothEA for functional annotation of transcriptomes.