Simultaneous Enrichment Analysis with rSEA | Overview of the Method | Defining the unified null hypothesis | Usage | Input and format | Example dataset | setTDP() function | setTest() function | SEA() function | topSEA() function | Creating the Pathlists | GO pathways | KEGG pathways | Wikipathways | Citing rSEA
Package: rSEA 2.1.2
Mitra Ebrahimpoor
rSEA: Simultaneous Enrichment Analysis
SEA performs simultaneous feature-set testing for (gen)omics data. It tests the unified null hypothesis and controls the family-wise error rate for all possible pathways. The unified null hypothesis is defined as: "The proportion of true features in the set is less than or equal to a threshold." Family-wise error rate control is provided through use of closed testing with Simes test. There are some practical functions to play around with the pathways of interest.
Authors:
rSEA_2.1.2.tar.gz
rSEA_2.1.2.zip(r-4.7-any)rSEA_2.1.2.zip(r-4.6-any)rSEA_2.1.2.zip(r-4.5-any)
rSEA_2.1.2.tgz(r-4.6-any)rSEA_2.1.2.tgz(r-4.5-any)
rSEA_2.1.2.tar.gz(r-4.7-any)rSEA_2.1.2.tar.gz(r-4.6-any)
rSEA_2.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rSEA/json (API)
| # Install 'rSEA' in R: |
| install.packages('rSEA', repos = c('https://mitra-ep.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mitra-ep/rsea/issues
Last updated from:e1da2d83d9. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 187 | ||
| source / vignettes | OK | 172 | ||
| linux-release | NOTE | 118 | ||
| macos-release | NOTE | 159 | ||
| macos-oldrel | NOTE | 207 | ||
| windows-devel | NOTE | 73 | ||
| windows-release | NOTE | 76 | ||
| windows-oldrel | NOTE | 70 | ||
| wasm-release | OK | 108 |
Exports:plotSEASEAsetTDPsetTesttopSEA
Dependencies:clicpp11farverggplot2gluegtablehommelisobandlabelinglifecycleR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simultaneous Enrichment Analysis (SEA) of all possible feature-sets using the unified null hypothesis | rSEA-package |
| topSEA | plotSEA |
| SEA | SEA |
| setTDP | setTDP |
| setTest | setTest |
| topSEA | topSEA |