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psSubpathway  

Flexible Identification of Phenotype-Specific Subpathways
View on CRAN: Click here


Download and install psSubpathway package within the R console
Install from CRAN:
install.packages("psSubpathway")

Install from Github:
library("remotes")
install_github("cran/psSubpathway")

Install by package version:
library("remotes")
install_version("psSubpathway", "0.1.3")



Attach the package and use:
library("psSubpathway")
Maintained by
Junwei Han
[Scholar Profile | Author Map]
First Published: 2019-06-21
Latest Update: 2023-08-09
Description:
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.
How to cite:
Junwei Han (2019). psSubpathway: Flexible Identification of Phenotype-Specific Subpathways. R package version 0.1.3, https://cran.r-project.org/web/packages/psSubpathway. Accessed 07 May. 2025.
Previous versions and publish date:
0.1.0 (2019-06-21 09:20), 0.1.1 (2019-10-02 14:40), 0.1.2 (2023-08-09 12:50)
Other packages that cited psSubpathway R package
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Complete documentation for psSubpathway
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