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'))

Peer review:

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 140 downloads 3 exports 80 dependencies

Last updated 3 months agofrom:d2ff8d1943. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKDec 30 2024
R-4.5-winOKDec 31 2024
R-4.5-linuxOKDec 30 2024
R-4.4-winOKDec 31 2024
R-4.4-macOKDec 30 2024
R-4.3-winOKDec 31 2024
R-4.3-macOKDec 30 2024

Exports:plotFindingsRolDERolDE_Main

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelbootclicodetoolscolorspacecpp11crayoncurlDelayedArraydigestdoParalleldoRNGfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeminqamunsellnlmenloptropensslpillarpkgconfigplyrqvalueR6RColorBrewerRcppRcppEigenreshape2rlangrngtoolsROTSS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVector

Introduction to the Robust longitudinal Differential Expression (RolDE) method

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Dec 30 2024.

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