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:Ryan C. Sartor <[email protected]>, Kathleen Greenham <[email protected]>

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'))

Peer review:

Datasets:
  • exampleData - Example Data: Data for use with the DiPALM vignette
  • testData - Test Data: Data for function testing

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 214 downloads 1 mentions 7 exports 106 dependencies

Last updated 2 years agofrom:20f3f52f01. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 14 2024
R-4.5-winOKOct 14 2024
R-4.5-linuxOKOct 14 2024
R-4.4-winOKOct 14 2024
R-4.4-macOKOct 14 2024
R-4.3-winOKOct 14 2024
R-4.3-macOKOct 14 2024

Exports:AdjustPvalueBlankPlotBuildLimmaLMBuildModMembershipggPlotMultiDensitiesPlotTCsPlotTCsRibbon

Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdoParalleldynamicTreeCutevaluatefansifarverfastclusterfastmapfontawesomeforeachforeignFormulafsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclelimmamagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngpreprocessCoreR6rappdirsRColorBrewerRcpprlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalesstatmodstringistringrsurvivalsystibbletinytexUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunXVectoryamlzlibbioc