1 Along signal paths: an empirical gene set approach exploiting pathway topology | 2 Performing pathway analysis | 3 Performing clipper analysis | 4 Visualizing clipper results. | 5 Easy clipper analysis | 6 Bibliography
Package: clipper 1.53.0
Paolo Martini
clipper: Gene Set Analysis Exploiting Pathway Topology
Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.
Authors:
clipper_1.53.0.tar.gz
clipper_1.53.0.zip(r-4.7)clipper_1.53.0.zip(r-4.6)clipper_1.53.0.zip(r-4.5)
clipper_1.53.0.tgz(r-4.6-any)clipper_1.53.0.tgz(r-4.5-any)
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clipper_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
clipper/json (API)
| # Install 'clipper' in R: |
| install.packages('clipper', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:clipper-1.53.0(bioc 3.24)clipper-1.52.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:19b96ff090. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 296 | ||
| linux-devel-x86_64 | OK | 440 | ||
| source / vignettes | OK | 339 | ||
| linux-release-x86_64 | OK | 459 | ||
| macos-release-arm64 | OK | 332 | ||
| macos-oldrel-arm64 | OK | 258 | ||
| windows-devel | OK | 423 | ||
| windows-release | OK | 348 | ||
| windows-oldrel | OK | 431 | ||
| wasm-release | OK | 208 |
Exports:clipperclipperAllRootscliqueMeanTestcliqueMixedTestcliquePairedTestcliqueVarianceTestdeleteEdgeeasyClipeasyLookgetGraphEntryGenesgetJunctionTreePathsnameCliquespathQplotInCytoscapeprunePaths
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscorpcorcpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphgRbasehttrigraphIRangesjsonliteKEGGgraphKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormopensslpkgconfigpngqpgraphqtlR6RcppRcppArmadilloRcppEigenRCurlrestfulrRgraphvizRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysvctrsXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dissect the pathway to find the path with the greatest association with phenotype. | clipper |
| Dissect the pathway to find the path with the greatest association with phenotype. | clipperAllRoots |
| Mean test for cliques. | cliqueMeanTest |
| Mean test for cliques. | cliqueMixedTest |
| Paired mean test for cliques. | cliquePairedTest |
| Variance test for cliques. | cliqueVarianceTest |
| Remove an edge from 'graphNel' object. | deleteEdge |
| Easy clip analysis. | easyClip |
| Summarize clipper output. | easyLook |
| Extract all the possible entry point (genes with no entering edges) from graph. | getGraphEntryGenes |
| Extract the shortest paths along the junction tree of the graph. | getJunctionTreePaths |
| Generate clique names from their own elements. | nameCliques |
| Whole pathway test using qpipf. | pathQ |
| Plot a pathway graph in Cytoscape highlighting the relevant path. | plotInCytoscape |
| Summarize the paths obtained by clipper according to their similarity. | prunePaths |
