Introduction | Pre-requisite Packages | Data Requirements | Example | References
Package: AGDEX 1.61.0
Cuilan lani Gao
AGDEX: Agreement of Differential Expression Analysis
A tool to evaluate agreement of differential expression for cross-species genomics
Authors:
AGDEX_1.61.0.tar.gz
AGDEX_1.61.0.zip(r-4.7)AGDEX_1.61.0.zip(r-4.6)AGDEX_1.61.0.zip(r-4.5)
AGDEX_1.61.0.tgz(r-4.6-any)AGDEX_1.61.0.tgz(r-4.5-any)
AGDEX_1.61.0.tar.gz(r-4.7-any)AGDEX_1.61.0.tar.gz(r-4.6-any)
AGDEX_1.61.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
AGDEX/json (API)
| # Install 'AGDEX' in R: |
| install.packages('AGDEX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- agdex.res - Saved result returned by agdex
- gset.data - A sample gene-set data
- human.data - Sample ExpressionSet object of human data
- map.data - Probe-set Mapping Data
- mouse.data - Mouse Data
On BioConductor:AGDEX-1.61.0(bioc 3.24)AGDEX-1.60.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraygeneticsgeneexpression
Last updated from:9fd2c8f801. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 161 | ||
| linux-devel-x86_64 | NOTE | 224 | ||
| source / vignettes | OK | 218 | ||
| linux-release-x86_64 | NOTE | 176 | ||
| macos-release-arm64 | NOTE | 146 | ||
| macos-oldrel-arm64 | NOTE | 122 | ||
| windows-devel | NOTE | 104 | ||
| windows-release | NOTE | 107 | ||
| windows-oldrel | NOTE | 109 | ||
| wasm-release | OK | 108 |
Exports:agdexagdex.scatterplotget.gset.result.detailsmake.dex.set.objectread.agdex.gset.detailsread.agdex.resultwrite.agdex.gset.detailswrite.agdex.result
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsgluegraphGSEABasehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigpngR6rlangRSQLiteS4VectorsSeqinfosysvctrsXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Agreement of differential expression analysis | AGDEX-package |
| Agreement of Differential Expression Analysis | agdex |
| Saved result returned by agdex() | agdex.res |
| scatter plot of AGDEX result | agdex.scatterplot |
| Extract gene-level details from gene-set results | get.gset.result.details |
| a sample gene-set data | gset.data |
| Sample ExpressionSet object of human data | human.data |
| Make a list object for function agdex() | make.dex.set.object |
| Probe-set Mapping Data | map.data |
| Mouse Data | mouse.data |
| read detailed results of gene-set analyses | read.agdex.gset.details |
| Read the output file of agdex analysis | read.agdex.result |
| write the output of get.gset.result.details to a tab-delimited text file. | write.agdex.gset.details |
| Write the AGDEX results to output file | write.agdex.result |