Package: DiPALM 1.2
DiPALM: Differential Pattern Analysis via Linear Modeling
Individual gene expression patterns are encoded into a series of eigenvector patterns ('WGCNA' package). Using the framework of linear model-based differential expression comparisons ('limma' package), time-course expression patterns for genes in different conditions are compared and analyzed for significant pattern changes. For reference, see: Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC and McClung CR. eLife. 2020 Sep 30;9(4). <doi:10.7554/eLife.58993>.
Authors:
DiPALM_1.2.tar.gz
DiPALM_1.2.zip(r-4.5)DiPALM_1.2.zip(r-4.4)DiPALM_1.2.zip(r-4.3)
DiPALM_1.2.tgz(r-4.4-any)DiPALM_1.2.tgz(r-4.3-any)
DiPALM_1.2.tar.gz(r-4.5-noble)DiPALM_1.2.tar.gz(r-4.4-noble)
DiPALM_1.2.tgz(r-4.4-emscripten)DiPALM_1.2.tgz(r-4.3-emscripten)
DiPALM.pdf |DiPALM.html✨
DiPALM/json (API)
| # Install 'DiPALM' in R: |
| install.packages('DiPALM', repos = c('https://humanoidtyphoon.r-universe.dev', 'https://cloud.r-project.org')) |
- exampleData - Example Data: Data for use with the DiPALM vignette
- testData - Test Data: Data for function testing
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:20f3f52f01. Checks:OK: 6 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 13 2024 |
| R-4.5-win | OK | Nov 13 2024 |
| R-4.5-linux | WARNING | Nov 13 2024 |
| R-4.4-win | OK | Nov 13 2024 |
| R-4.4-mac | OK | Nov 13 2024 |
| R-4.3-win | OK | Nov 13 2024 |
| R-4.3-mac | OK | Nov 13 2024 |
Exports:AdjustPvalueBlankPlotBuildLimmaLMBuildModMembershipggPlotMultiDensitiesPlotTCsPlotTCsRibbon
Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdoParalleldynamicTreeCutevaluatefansifarverfastclusterfastmapfontawesomeforeachforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclelimmamagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngpreprocessCoreR6rappdirsRColorBrewerRcpprlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalesstatmodstringistringrsurvivalsystibbletinytexUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DiPALM - Differential Pattern Analysis via Linear Modeling | DiPALM-package DiPALM |
| Determine p-values based on permutation test results | AdjustPvalue |
| Generate a blank plot window | BlankPlot |
| Fit linear models to time-course expression patterns using the limma package | BuildLimmaLM |
| Calculate module membership (kME) for all genes in a time-course data set | BuildModMembership |
| Example Data: Data for use with the DiPALM vignette | exampleData |
| Plot multiple density distributions | ggPlotMultiDensities |
| Plot multiple time-course expression patterns for one gene | PlotTCs |
| Plot multiple averaged time-course expression patterns for a group of genes | PlotTCsRibbon |
| Test Data: Data for function testing | testData |
