ssgsea

<p>Single sample GSEA (ssGSEA) calculates a gene set enrichment score
per sample as the normalized difference in empirical cumulative distribution
functions of gene expression ranks inside and outside the gene set.</p>

A network-based systems biology tool for flexible identification of phenotype-specific subpathways in the cancer gene expression data
with multiple categories (such as multiple subtype or developmental stages of cancer). Subtype Set Enrichment Analysis (SubSEA) and Dynamic Changed
Subpathway Analysis (DCSA) are developed to flexible identify subtype specific and dynamic changed subpathways respectively. The operation modes
include extraction of subpathways from biological pathways, inference of subpathway activities in the context of gene expression data, identification
of subtype specific subpathways with SubSEA, identification of dynamic changed subpathways associated with the cancer developmental stage with DCSA,
and visualization of the activities of resulting subpathways by using box plots and heat maps. Its capabilities render the tool could find the specific
abnormal subpathways in the cancer dataset with multi-phenotype samples.

Junwei Han

psSubpathway

Flexible Identification of Phenotype-Specific Subpathways

ssgsea function

<p>Xudong Han,
Junwei Han,
Qingfei Kong</p>

ssgsea: psSubpathway internal functions

Description

Usage

Arguments

Author

Details