1. Introduction | 2. Installation and Quick Start | 2.1 Installing GSALightning | 2.2 Running GSALightning | 3. The Inputs for GSALight() | 4. GSALight() | 4.1 Preliminiary Data Check | 4.2 Most Commonly Considered Arguments for GSALight() | 4.3 The Maxmean, Mean, and Absolute Mean Statistics | 4.4 Outputs of GSALight() | 4.5 Default Number of Permutations | 4.6 Restandardization | 5. Other Functions in GSALightning | 5.1 Single Gene Permutation Test | 5.2 Mann-Whitney U Test for Single Gene Testing | 5.3 Gene Set Analysis for Paired Design | References
Package: GSALightning 1.41.0
Billy Heung Wing Chang
GSALightning: Fast Permutation-based Gene Set Analysis
GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.
Authors:
GSALightning_1.41.0.tar.gz
GSALightning_1.41.0.zip(r-4.7)GSALightning_1.41.0.zip(r-4.6)GSALightning_1.41.0.zip(r-4.5)
GSALightning_1.41.0.tgz(r-4.6-any)GSALightning_1.41.0.tgz(r-4.5-any)
GSALightning_1.41.0.tar.gz(r-4.7-any)GSALightning_1.41.0.tar.gz(r-4.6-any)
GSALightning_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GSALightning/json (API)
| # Install 'GSALightning' in R: |
| install.packages('GSALightning', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/billyhw/gsalightning/issues
Datasets:
- expression - Breast Cancer Data from The Cancer Genome Atlas
- sampleInfo - Sample Information for the Breast Cancer Data from The Cancer Genome Atlas
- targetGenes - Target Genes of Distal Regulatory Elements
On BioConductor:GSALightning-1.41.0(bioc 3.24)GSALightning-1.40.0(bioc 3.23)
softwarebiologicalquestiongenesetenrichmentdifferentialexpressiongeneexpressiontranscription
Last updated from:78491b99c4. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 145 | ||
| linux-devel-x86_64 | NOTE | 179 | ||
| source / vignettes | OK | 178 | ||
| linux-release-x86_64 | NOTE | 149 | ||
| macos-release-arm64 | NOTE | 80 | ||
| macos-oldrel-arm64 | NOTE | 89 | ||
| windows-devel | NOTE | 96 | ||
| windows-release | NOTE | 84 | ||
| windows-oldrel | NOTE | 83 | ||
| wasm-release | OK | 96 |
Exports:GSALightpermTestLightwilcoxTest
Dependencies:data.tablelatticeMatrix
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fast Permutation-based Gene Set Analysis | GSALightning-package GSALightning |
| Breast Cancer Data from The Cancer Genome Atlas (TCGA) | expression |
| Fast Permutation-based Gene Set Analysis | GSALight |
| Fast Single-Gene Permutation Test | permTestLight |
| Sample Information for the Breast Cancer Data from The Cancer Genome Atlas (TCGA) | sampleInfo |
| Target Genes of Distal Regulatory Elements | targetGenes |
| Single-Gene Mann Whitney Wilcoxon Test | wilcoxTest |
