clipper specifications


Unique identifier OMICS_14763
Name clipper
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.20.1
Stability Stable
methods, BiocGenerics, Biobase, Matrix, R(>=2.15.0), BiocStyle, Rcpp, RUnit, MASS, corpcor, graph, RBGL, KEGGgraph, hgu95av2.db, igraph, ALL, graphite, qpgraph, gRbase(>=1.6.6)
Maintained Yes




No version available



  • person_outline Chiara Romualdi
  • person_outline Paolo Martini

Publication for clipper

clipper citations


Prioritizing biological pathways by recognizing context in time series gene expression data

BMC Bioinformatics
PMCID: 5259824
PMID: 28155707
DOI: 10.1186/s12859-016-1335-8

[…] distributed or over-represented either at the top or bottom of the ranked list []. PT-based methods use the topology of a pathway where genes are nodes and their interactions are edges. For instance, CliPPER selects significant pathways based on the network represented as the mean and covariance matrix and determines fraction of signaling paths that are correlated with phenotypes [].Recently, time […]


Pathway based Analysis Tools for Complex Diseases: A Review

PMCID: 4411419
PMID: 25462153
DOI: 10.1016/j.gpb.2014.10.002

[…] n test (LCT) and supervised principal component analysis (SPCA) . Recently, some topological methods to parse the internal information of pathway (e.g., signaling pathway impact analysis (SPIA) and CliPPER ) have also been developed. In short, pathway-based analysis has gradually become an advanced way to the analysis of complex diseases .With the methodological advance, application of pathway-b […]

clipper institution(s)
CRIBI Biotechnology Center, University of Padova, Padova, Italy; Department of Biology, University of Padova, Padova, Italy; Department of Statistics, University of Oxford, Oxford, UK; Department of Statistical Science, University of Padova, Padova, Italy
clipper funding source(s)
Supported by University of Padova [CPDR075919, CPDA119031 and CPDR070805].

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