Introduction | Example | Comparing state-specific PANDA networks | Other helpful functions | Session information
Package: pandaR 1.45.0
Joseph N. Paulson
pandaR: PANDA Algorithm
Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.
Authors:
pandaR_1.45.0.tar.gz
pandaR_1.45.0.zip(r-4.7)pandaR_1.45.0.zip(r-4.6)pandaR_1.45.0.zip(r-4.5)
pandaR_1.45.0.tgz(r-4.6-any)pandaR_1.45.0.tgz(r-4.5-any)
pandaR_1.45.0.tar.gz(r-4.7-any)pandaR_1.45.0.tar.gz(r-4.6-any)
pandaR_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
pandaR/json (API)
| # Install 'pandaR' in R: |
| install.packages('pandaR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- pandaResult - Analysis result from PANDA algorithm on toy data
- pandaResultPairs - Analysis result from PANDA algorithm on toy data converted into pairs
- pandaToyData - Toy gene expression, motif, and ppi data
On BioConductor:pandaR-1.45.0(bioc 3.24)pandaR-1.44.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
statisticalmethodgraphandnetworkmicroarraygeneregulationnetworkinferencegeneexpressiontranscriptionnetwork
Last updated from:c5adcb5da7. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.
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|---|---|---|---|---|
| bioc-checks | ERROR | 202 | ||
| linux-devel-x86_64 | WARNING | 224 | ||
| source / vignettes | ERROR | 189 | ||
| linux-release-x86_64 | WARNING | 186 | ||
| macos-release-arm64 | WARNING | 89 | ||
| macos-oldrel-arm64 | WARNING | 119 | ||
| windows-devel | WARNING | 108 | ||
| windows-release | WARNING | 128 | ||
| windows-oldrel | WARNING | 100 | ||
| wasm-release | OK | 146 |
Exports:calcDegreecalcDegreeDifferenceimportPandaMatlabmultiplotpandaplotCommunityDetectionplotGraphplotZplotZbyTFsubnetworksummary.pandatargetedGenestestMotiftopedges
Dependencies:BiobaseBiocGenericsclicpp11farvergenericsggplot2gluegtablehexbinigraphisobandlabelinglatticelifecyclemagrittrMatrixmatrixStatspkgconfigplyrR6RColorBrewerRcppreshaperlangRUnitS7scalesvctrsviridisLitewithr
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
An Introduction to the pandaR Package
Last update: 2016-05-01
Started: 2015-04-06
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate regulatory network degree | calcDegree |
| Calculate difference in degrees | calcDegreeDifference |
| Panda Matlab importer | importPandaMatlab |
| Multiple plots | multiplot |
| Passing Messages between Biological Networks to Refine Predicted Interactions | panda |
| pandaR: Passing Messages between Biological Networks to Refine Predicted Interactions. | pandaR-package pandaR |
| Analysis result from PANDA algorithm on toy data | pandaResult |
| Analysis result from PANDA algorithm on toy data converted into pairs | pandaResultPairs |
| Toy gene expression, motif, and ppi data | pandaToyData |
| Community detection plot | plotCommunityDetection |
| Plot graph | plotGraph |
| Comparison of Z scores between two PANDA runs | plotZ |
| Plot Z by TF out-degree quantiles | plotZbyTF |
| print.panda | print.panda |
| Subnetwork | subnetwork |
| Summary.panda | summary.panda |
| targetedGenes | targetedGenes |
| Check motif | testMotif |
| Top edges | topedges |