Package: aPEAR 1.0.0

Ieva Kerseviciute

aPEAR: Advanced Pathway Enrichment Analysis Representation

Simplify pathway enrichment analysis results by detecting clusters of similar pathways and visualizing it as an enrichment network, where nodes and edges describe the pathways and similarity between them, respectively. This reduces the redundancy of the overlapping pathways and helps to notice the most important biological themes in the data (Kerseviciute and Gordevicius (2023) <doi:10.1101/2023.03.28.534514>).

Authors:Ieva Kerseviciute [aut, cre], Juozas Gordevicius [ths], VUGENE, LLC [cph, fnd]

aPEAR_1.0.0.tar.gz
aPEAR_1.0.0.zip(r-4.5)aPEAR_1.0.0.zip(r-4.4)aPEAR_1.0.0.zip(r-4.3)
aPEAR_1.0.0.tgz(r-4.4-any)aPEAR_1.0.0.tgz(r-4.3-any)
aPEAR_1.0.0.tar.gz(r-4.5-noble)aPEAR_1.0.0.tar.gz(r-4.4-noble)
aPEAR_1.0.0.tgz(r-4.4-emscripten)aPEAR_1.0.0.tgz(r-4.3-emscripten)
aPEAR.pdf |aPEAR.html✨
aPEAR/json (API)
NEWS

# Install 'aPEAR' in R:
install.packages('aPEAR', repos = c('https://cranhaven.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://gitlab.com/vugene/apear

On CRAN:

archivedpackagesr-universe

3.74 score 5 stars 22 scripts 412 downloads 5 exports 51 dependencies

Last updated 11 days agofrom:06a6a87b8f (on package/aPEAR). Checks:5 OK, 2 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 10 2025
R-4.5-winOKJan 10 2025
R-4.5-linuxOKJan 10 2025
R-4.4-winOKJan 10 2025
R-4.4-macOKJan 10 2025
R-4.3-winNOTEJan 10 2025
R-4.3-macNOTEJan 10 2025

Exports:aPEAR.methodsaPEAR.themeenrichmentNetworkfindPathClustersplotPathClusters

Dependencies:arulesbayesbioclicolorspacecpp11data.tabledplyrexpmfansifarvergenericsggforceggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclelsamagrittrMASSMatrixMCLmgcvmunsellnlmepillarpkgconfigplyrpolyclipR6RColorBrewerRcppRcppEigenreshape2rlangscalesSnowballCstringistringrsystemfontstibbletidyselecttweenrutf8vctrsviridisLitewithr

An introduction to aPEAR

Ieva Kerseviciute

Rendered fromaPEAR-vignette.Rmdusingknitr::rmarkdownon Jan 10 2025.

Last update: 2025-01-10
Started: 2025-01-10