Package: pageRank 1.15.0

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:Hongxu Ding [aut, cre, ctb, cph]

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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-1.15.0(bioc 3.20)pageRank-1.14.0(bioc 3.19)

bioconductor-package

12 exports 0.36 score 119 dependencies

Last updated 2 months agofrom:36e05764f0

Exports:accessibility_network adjust_graph aracne_network bubble_plot clean_graph conformation_network diff_graph get_color_gradient multiplex_page_rank P_graph P_null time_expmat

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools cli clipr CNEr codetools colorspace cpp11 crayon curl DBI DelayedArray DirichletMultinomial fansi farver fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue GO.db gtable gtools hms httr igraph IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime motifmatchr munsell nlme openssl pillar pkgconfig plogr plyr png poweRlaw pracma prettyunits progress pwalign R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales seqLogo snow SparseArray stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xtable XVector yaml zlibbioc

pageRank

Rendered fromintroduction.rnwusingutils::Sweaveon Jun 21 2024.

Last update: 2020-09-15
Started: 2020-09-04

Citation

Development and contributors

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