Package description | Reference | Input gene expression data format | Input gene set data format | To load the package: | Example 1: | Example 2:
Package: decode 1.2
Thomas Lui
decode: Differential Co-Expression and Differential Expression Analysis
Integrated differential expression (DE) and differential co-expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-expression and Differential Expression) algorithm.
Authors:
decode_1.2.tar.gz
decode_1.2.tar.gz(r-4.7-any)decode_1.2.tar.gz(r-4.6-any)
decode_1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
decode/json (API)
| # Install 'decode' in R: |
| install.packages('decode', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:5e6a29b324. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 141 | ||
| source / vignettes | OK | 131 | ||
| linux-release-x86_64 | OK | 141 | ||
| wasm-release | OK | 106 |
Exports:getAssoGeneSetPValuegetBestAssociatedGeneSetgetBonferroniPValuegetDE_DC_OptimalThresholdgetFDRgetPartitionIndexgetPathwayopenFileToWriterunDecodesumResult_MinGain
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate the p-value between selected genes and functional gene set | getAssoGeneSetPValue |
| Get best associated functional gene sets for partitions of gene i | getBestAssociatedGeneSet |
| Adjust p-value by Bonferroni correction | getBonferroniPValue |
| Perform chi-square optimization | getDE_DC_OptimalThreshold |
| Adjust p-value by Benjamini and Hochberg method | getFDR |
| Get gene index of 8 partitions for gene i | getPartitionIndex |
| read functional gene sets | getPathway |
| Open file to write result | openFileToWrite |
| Differential Co-Expression and Differential Expression Analysis | runDecode |
| Summarize the functional gene set results into text file | sumResult_MinGain |