Introduction | Installation | Applying RolDE in example datasets with aligned time points | Semi-simulated spike-in dataset | Applying RolDE in example data with non aligned time points | Changing the settings for RolDE | Preparation of data for RolDE | References
Package: RolDE 1.17.0
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:
RolDE_1.17.0.tar.gz
RolDE_1.17.0.zip(r-4.7)RolDE_1.17.0.zip(r-4.6)RolDE_1.17.0.zip(r-4.5)
RolDE_1.17.0.tgz(r-4.6-any)RolDE_1.17.0.tgz(r-4.5-any)
RolDE_1.17.0.tar.gz(r-4.7-any)RolDE_1.17.0.tar.gz(r-4.6-any)
RolDE_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RolDE/json (API)
| # 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-1.17.0(bioc 3.24)RolDE-1.16.0(bioc 3.23)
statisticalmethodsoftwaretimecourseregressionproteomicsdifferentialexpression
Last updated from:6cb224542c. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 181 | ||
| linux-devel-x86_64 | OK | 398 | ||
| source / vignettes | OK | 240 | ||
| linux-release-x86_64 | OK | 396 | ||
| macos-release-arm64 | OK | 197 | ||
| macos-oldrel-arm64 | OK | 188 | ||
| windows-devel | OK | 314 | ||
| windows-release | OK | 290 | ||
| windows-oldrel | OK | 331 | ||
| wasm-release | OK | 154 |
Exports:plotFindingsRolDERolDE_Main
Dependencies:abindBHBiobaseBiocGenericsBiocParallelbootclicodetoolscpp11DelayedArraydigestdoParalleldoRNGfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobanditeratorslabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsminqanlmenloptrplyrqvalueR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2rlangrngtoolsROTSS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsurvivalvctrsviridisLitewithrXVector
