pathfindR

Pathway Enrichment Analysis Utilizing Active Subnetworks

Pathway enrichment analysis enables researchers to uncover mechanisms underlying the phenotype. pathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies active subnetworks in a protein-protein interaction network using user-provided a list of genes. It performs pathway enrichment analyses on the identified subnetworks. pathfindR also offers functionalities to cluster enriched pathways and identify representative pathways and to score the pathways per sample. The method is described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv. <doi:10.1101/272450>.

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Description file content

Package
pathfindR
Type
Package
Title
Pathway Enrichment Analysis Utilizing Active Subnetworks
Version
1.2.2
Author
Ege Ulgen, Ozan Ozisik
Maintainer
Ege Ulgen
Description
Pathway enrichment analysis enables researchers to uncover mechanisms underlying the phenotype. pathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies active subnetworks in a protein-protein interaction network using user-provided a list of genes. It performs pathway enrichment analyses on the identified subnetworks. pathfindR also offers functionalities to cluster enriched pathways and identify representative pathways and to score the pathways per sample. The method is described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv. .
License
MIT + file LICENSE
URL
BugReports
https://github.com/egeulgen/pathfindR/issues
Encoding
UTF-8
LazyData
true
SystemRequirements
Java JVM 1.8
Imports
AnnotationDbi, DBI, doParallel, foreach, rmarkdown, org.Hs.eg.db, ggplot2, fpc
Depends
R (>= 3.4), knitr, shiny, pathview
RoxygenNote
6.1.0
VignetteBuilder
knitr
NeedsCompilation
no
Packaged
2018-10-04 19:24:11 UTC; egeulgen
Repository
CRAN
Date/Publication
2018-10-04 23:00:03 UTC

install.packages('pathfindR')

1.2.2

10 days ago

https://github.com/egeulgen/pathfindR

Ege Ulgen

MIT + file LICENSE

Depends on

R (>= 3.4), knitr, shiny, pathview

Imports

AnnotationDbi, DBI, doParallel, foreach, rmarkdown, org.Hs.eg.db, ggplot2, fpc

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