Package: pageRank 1.17.0
Hongxu Ding
pageRank: Temporal and Multiplex PageRank for Gene Regulatory Network Analysis
Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.
Authors:
pageRank_1.17.0.tar.gz
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pageRank_1.17.0.tgz(r-4.4-any)pageRank_1.17.0.tgz(r-4.3-any)
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pageRank.pdf |pageRank.html✨
pageRank/json (API)
NEWS
| # Install 'pageRank' in R: |
| install.packages('pageRank', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hd2326/pagerank/issues
On BioConductor:pageRank-1.17.0(bioc 3.21)pageRank-1.16.0(bioc 3.20)
statisticalmethodgenetargetnetwork
Last updated 2 months agofrom:a33df28ffc. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:accessibility_networkadjust_grapharacne_networkbubble_plotclean_graphconformation_networkdiff_graphget_color_gradientmultiplex_page_rankP_graphP_nulltime_expmat
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolsclicliprCNErcodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDirichletMultinomialfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2glueGO.dbgtablegtoolshmshttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemotifmatchrmunsellnlmeopensslpillarpkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogresspwalignR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesseqLogosnowSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build Network from Accessibility Peaks. | accessibility_network |
| Re-calculate PageRank | adjust_graph |
| Re-format ARACNe Network. | aracne_network |
| Make Bubbleplot | bubble_plot |
| Clean Graph | clean_graph |
| Build Network from Conformation Peaks. | conformation_network |
| Calculate Temporal PageRank from Two Graphs | diff_graph |
| Generate Color Gradient | get_color_gradient |
| Calculate Multiplex PageRank | multiplex_page_rank |
| Build Probability-Based Network | P_graph |
| Build Null Distribution of Probability-Based Distance | P_null |
| Generate Timewise Average Gene Expression | time_expmat |