quantiseqr

quantiseqr quantifies the Tumor Immune contexture from RNA-seq data by implementing the quanTIseq method against the TIL10 signature to dissect the contributions of ten immune cell types.

Key Features:

• TIL10 Signature Quantification: Performs deconvolution against the TIL10 signature, which was carefully crafted from a collection of human RNA-seq samples.
• Ten Immune Cell Type Deconvolution: Dissects the contributions of ten distinct immune cell types from bulk RNA-seq data.
• Extensive Signature Validation: The TIL10 signature has been validated using simulated data, flow cytometry data, and immunohistochemistry data.

Scientific Applications:

• Tumor Immune Contexture Analysis: Enables quantification of tumor-infiltrating lymphocyte compositions from cancer RNA-seq datasets.
• Immuno-oncology Research: Supports investigation of immune cell infiltration patterns in human tumor samples.

Methodology:

The package provides a streamlined workflow for the quanTIseq method, performing quantification of immune cell fractions from RNA-seq data using the TIL10 signature.