Package: aPEAR 1.0.0

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://kerseviciute.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On CRAN:

4.00 score 20 scripts 336 downloads 5 exports 51 dependencies

Last updated 1 years agofrom:fd4a13ef98. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:aPEAR.methodsaPEAR.themeenrichmentNetworkfindPathClustersplotPathClusters

Dependencies:arulesbayesbioclicolorspacecpp11data.tabledplyrexpmfansifarvergenericsggforceggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclelsamagrittrMASSMatrixMCLmgcvmunsellnlmepillarpkgconfigplyrpolyclipR6RColorBrewerRcppRcppEigenreshape2rlangscalesSnowballCstringistringrsystemfontstibbletidyselecttweenrutf8vctrsviridisLitewithr

An introduction to aPEAR

Ieva Kerseviciute

Rendered fromaPEAR-vignette.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2023-06-08
Started: 2023-06-06