Package: pageRank 1.23.0

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]

pageRank_1.23.0.tar.gz
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pageRank_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pageRank/json (API)

# 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-1.23.0(bioc 3.24)pageRank-1.22.0(bioc 3.23)

statisticalmethod genetarget network

3.30 score 7 scripts 12 exports 76 dependencies

Last updated from:400b824fb8. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	378
linux-devel-x86_64	NOTE	457
source / vignettes	OK	377
linux-release-x86_64	NOTE	454
macos-release-arm64	NOTE	247
macos-oldrel-arm64	NOTE	250
windows-devel	NOTE	343
windows-release	NOTE	395
windows-oldrel	NOTE	368
wasm-release	OK	295

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 askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools cigarillo cli codetools cpp11 crayon curl DBI DelayedArray DirichletMultinomial fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue gtools httr igraph IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime motifmatchr openssl pkgconfig pwalign R6 Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo seqLogo snow SparseArray SummarizedExperiment sys TFBSTools TFMPvalue vctrs XML XVector yaml

pageRank

Introduction | PageRank Analysis | Prioritizing TFs in GRNs | References

Rendered fromintroduction.rnwusingutils::Sweave

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