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

Peer review:

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

On CRAN:

5 exports 0.66 score 51 dependencies 16 scripts 449 downloads

Last updated 12 months agofrom:fd4a13ef98. Checks:OK: 7. Indexed: yes.

Exports:aPEAR.methodsaPEAR.themeenrichmentNetworkfindPathClustersplotPathClusters

Dependencies:arulesbayesbioclicolorspacecpp11data.tabledplyrexpmfansifarvergenericsggforceggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclelsamagrittrMASSMatrixMCLmgcvmunsellnlmepillarpkgconfigplyrpolyclipR6RColorBrewerRcppRcppEigenreshape2rlangscalesSnowballCstringistringrsystemfontstibbletidyselecttweenrutf8vctrsviridisLitewithr