Package: RolDE 1.11.0

Medical Bioinformatics Centre

RolDE: RolDE: Robust longitudinal Differential Expression

RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings.

Authors:Tommi Valikangas [aut], Medical Bioinformatics Centre [cre]

RolDE_1.11.0.tar.gz
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RolDE.pdf |RolDE.html✨
RolDE/json (API)
NEWS

# Install 'RolDE' in R:
install.packages('RolDE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/elolab/rolde/issues

Datasets:
  • data1 - A proteomics dataset with random protein expression values - no missing values.
  • data2 - A small dataset with 50 proteins and 30 samples for the example usage of RolDE
  • data3 - A semi-simulated UPS1 spike-in dataset with differences in longitudinal expression for the spike-in proteins - no missing values.
  • des_matrix1 - A RolDE design matrix for data1
  • des_matrix2 - A RolDE design matrix for data2
  • des_matrix3 - A RolDE design matrix for data3
  • res1 - RolDE results for data1
  • res3 - RolDE results for data3

On BioConductor:RolDE-1.11.0(bioc 3.21)RolDE-1.10.0(bioc 3.20)

statisticalmethodsoftwaretimecourseregressionproteomicsdifferentialexpression

5.18 score 5 stars 1 scripts 178 downloads 3 exports 83 dependencies

Last updated 4 months agofrom:d2ff8d1943. Checks:7 OK, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winOKJan 29 2025
R-4.5-macWARNINGJan 29 2025
R-4.5-linuxOKJan 29 2025
R-4.4-winOKJan 29 2025
R-4.4-macOKJan 29 2025
R-4.3-winOKJan 29 2025
R-4.3-macOKJan 29 2025

Exports:plotFindingsRolDERolDE_Main

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelbootclicodetoolscolorspacecpp11crayoncurlDelayedArraydigestdoParalleldoRNGfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeminqamunsellnlmenloptropensslpillarpkgconfigplyrqvalueR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2rlangrngtoolsROTSS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVector

Introduction to the Robust longitudinal Differential Expression (RolDE) method

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2022-10-11
Started: 2021-04-09