Package: limorhyde2 0.1.0
Jake Hughey
limorhyde2: Quantify Rhythmicity and Differential Rhythmicity in Genomic Data
Fit linear models based on periodic splines, moderate model coefficients using multivariate adaptive shrinkage, then compute properties of the moderated curves.
Authors:
limorhyde2_0.1.0.tar.gz
limorhyde2_0.1.0.zip(r-4.5)limorhyde2_0.1.0.zip(r-4.4)limorhyde2_0.1.0.zip(r-4.3)
limorhyde2_0.1.0.tgz(r-4.4-any)limorhyde2_0.1.0.tgz(r-4.3-any)
limorhyde2_0.1.0.tar.gz(r-4.5-noble)limorhyde2_0.1.0.tar.gz(r-4.4-noble)
limorhyde2_0.1.0.tgz(r-4.4-emscripten)limorhyde2_0.1.0.tgz(r-4.3-emscripten)
limorhyde2.pdf |limorhyde2.html✨
limorhyde2/json (API)
NEWS
| # Install 'limorhyde2' in R: |
| install.packages('limorhyde2', repos = c('https://hugheylab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hugheylab/limorhyde2/issues
Last updated 11 months agofrom:ae55823ded. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 06 2024 |
| R-4.5-win | OK | Nov 06 2024 |
| R-4.5-linux | OK | Nov 06 2024 |
| R-4.4-win | OK | Nov 06 2024 |
| R-4.4-mac | OK | Nov 06 2024 |
| R-4.3-win | OK | Nov 06 2024 |
| R-4.3-mac | OK | Nov 06 2024 |
Exports:getDiffRhythmStatsgetExpectedMeasgetExpectedMeasIntervalsgetModelFitgetPosteriorFitgetPosteriorSamplesgetRhythmStatsgetStatsIntervalsmergeMeasMeta
Dependencies:abindashraskpassassertthatbackportsBHBiobaseBiocGenericsBiocParallelcheckmateclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDESeq2etrunctfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableHDIntervalhttrinvgammaIRangesirlbaisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrmashrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemixsqpmunsellmvtnormnlmeopensslpbspillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloRcppGSLrlangrmetaS4ArraysS4VectorsscalessnowsoftImputeSparseArraySQUAREMstatmodSummarizedExperimentsystibbletruncnormUCSC.utilsutf8vctrsviridisLitewithrXVectorzeallotzlibbioc
Analyzing RNA-seq data
Rendered fromrnaseq.Rmdusingknitr::rmarkdownon Nov 06 2024.Last update: 2022-04-11
Started: 2022-01-27
Quantifying differential rhythmicity between conditions
Rendered fromdifferential-rhythmicity.Rmdusingknitr::rmarkdownon Nov 06 2024.Last update: 2022-04-11
Started: 2021-07-19
Quantifying rhythmicity in one condition
Rendered fromrhythmicity.Rmdusingknitr::rmarkdownon Nov 06 2024.Last update: 2022-04-11
Started: 2021-07-19
Quantifying uncertainty in (differential) rhythmicity
Rendered fromuncertainty.Rmdusingknitr::rmarkdownon Nov 06 2024.Last update: 2022-04-11
Started: 2021-07-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute differential rhythm statistics from fitted models | getDiffRhythmStats |
| Compute expected measurements from fitted models | getExpectedMeas |
| Compute credible intervals for expected measurements | getExpectedMeasIntervals |
| Fit linear models for rhythmicity in one or more conditions | getModelFit |
| Compute posterior fit for linear models for rhythmicity | getPosteriorFit |
| Draw samples from posterior distributions of fitted models | getPosteriorSamples |
| Compute rhythm statistics from fitted models | getRhythmStats |
| Compute credible intervals for rhythm or differential rhythm statistics | getStatsIntervals |
| Gene expression data for GSE34018 | GSE34018 |
| Gene expression data for GSE54650 | GSE54650 |
| Merge measurements and metadata | mergeMeasMeta |
