PANDA: Preferential Attachment Based Common Neighbor Distribution Derived Functional Associations

PANDA (Preferential Attachment based common Neighbor Distribution derived Associations) is designed to perform the following tasks in PPI networks: (1) identify significantly functionally associated protein pairs, (2) predict GO terms and KEGG pathways for proteins, (3) make a cluster of proteins based on the significant protein pairs, (4) identify subclusters whose members are enriched in KEGG pathways. For other types of biological networks, (1) and (3) can still be performed.

Author
Hua Li and Pan Tong
Date of publication
2014-11-07 11:17:28
Maintainer
Hua Li <kaixinsjtu@hotmail.com>
License
Artistic-2.0
Version
0.9.9

View on CRAN

Man pages

dfPPI
An example of protein-protein interaction data
GENE2GOtopLite
An example of GO annotation data for proteins
GENE2KEGG
An example of KEGG annotation data for proteins
GOpredict-methods
Predict GO annotations for proteins
KEGGID2NAME
KEGG pathway ID to KEGG pathway name
KEGGpredict-methods
Predict KEGG pathway annotations for proteins
ProteinCluster-methods
Cluster proteins based on significant protein pairs
SignificantPairs-methods
Identify functionally associated protein pairs
SignificantSubcluster-methods
Subclusters with KEGG annotations significantly enriched

Files in this package

PANDA
PANDA/inst
PANDA/inst/doc
PANDA/inst/doc/PANDA.R
PANDA/inst/doc/PANDA.pdf
PANDA/inst/doc/PANDA.Rnw
PANDA/NAMESPACE
PANDA/data
PANDA/data/GENE2KEGG.rda
PANDA/data/KEGGID2NAME.rda
PANDA/data/GENE2GOtopLite.rda
PANDA/data/dfPPI.rda
PANDA/R
PANDA/R/dfPPI.r
PANDA/R/GENE2KEGG.r
PANDA/R/GENE2GOtopLite.r
PANDA/R/KEGGID2NAME.r
PANDA/R/FunctionScript.R
PANDA/vignettes
PANDA/vignettes/PANDA.Rnw
PANDA/README.md
PANDA/MD5
PANDA/build
PANDA/build/vignette.rds
PANDA/DESCRIPTION
PANDA/man
PANDA/man/GOpredict-methods.Rd
PANDA/man/dfPPI.Rd
PANDA/man/KEGGID2NAME.Rd
PANDA/man/SignificantSubcluster-methods.Rd
PANDA/man/SignificantPairs-methods.Rd
PANDA/man/GENE2KEGG.Rd
PANDA/man/ProteinCluster-methods.Rd
PANDA/man/KEGGpredict-methods.Rd
PANDA/man/GENE2GOtopLite.Rd