Package: DiPALM 1.3

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 [aut, cre], Kathleen Greenham [aut], William Gustafson [aut]

DiPALM_1.3.tar.gz
DiPALM_1.3.zip(r-4.7-any)DiPALM_1.3.zip(r-4.6-any)DiPALM_1.3.zip(r-4.5-any)
DiPALM_1.3.tgz(r-4.6-any)DiPALM_1.3.tgz(r-4.5-any)
DiPALM_1.3.tar.gz(r-4.7-any)DiPALM_1.3.tar.gz(r-4.6-any)
DiPALM_1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DiPALM/json (API)

# Install 'DiPALM' in R:
install.packages('DiPALM', repos = c('https://humanoidtyphoon.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • exampleData - Example Data: Data for use with the DiPALM vignette
  • smallTestData - Small test data for the DiPALM pipeline.
  • testData - Test Data: Data for function testing

On CRAN:

Conda:

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

1.00 score 405 downloads 1 mentions 16 exports 81 dependencies

Last updated from:c60e171aa0. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE197
source / vignettesOK169
linux-releaseNOTE209
macos-releaseNOTE341
macos-oldrelNOTE236
windows-develNOTE151
windows-releaseNOTE154
windows-oldrelNOTE136
wasm-releaseOK144

Exports:AdjustPvalueBlankPlotBuildLimmaLMBuildModMembershipcol_format_subdipalmggPlotMultiDensitiesjoinOutputsmainmake_TCsmsubopen_logPlotTCsPlotTCsRibbonre_escsampleReplicates

Dependencies:backportsbase64encBiocGenericsBiostringsbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayondata.tabledigestdoParalleldynamicTreeCutevaluatefarverfastclusterfastmapfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehashrhighrHmischtmlTablehtmltoolshtmlwidgetsimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelimmamagrittrMatrixmatrixStatsmemoisemimennetpreprocessCorepwalignR6rappdirsRColorBrewerRcpprlangrmarkdownrpartrstudioapiS4VectorsS7sassscalesSeqinfostatmodstringistringrsurvivaltinytexvctrsviridisLiteWGCNAwithrxfunXVectoryaml