Package: limorhyde2 0.1.1

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:Jake Hughey [aut, cre], Dora Obodo [aut], Elliot Outland [aut]

limorhyde2_0.1.1.tar.gz
limorhyde2_0.1.1.zip(r-4.7)limorhyde2_0.1.1.zip(r-4.6)limorhyde2_0.1.1.zip(r-4.5)
limorhyde2_0.1.1.tgz(r-4.6-any)limorhyde2_0.1.1.tgz(r-4.5-any)
limorhyde2_0.1.1.tar.gz(r-4.7-any)limorhyde2_0.1.1.tar.gz(r-4.6-any)
limorhyde2_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
limorhyde2/json (API)

# 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

Pkgdown/docs site:https://limorhyde2.hugheylab.org

Datasets:
  • GSE34018 - Gene expression data for GSE34018
  • GSE54650 - Gene expression data for GSE54650

On CRAN:

Conda:

4.78 score 1 stars 2 scripts 291 downloads 9 exports 70 dependencies

Last updated from:5a4b8bba9b. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK187
source / vignettesOK218
linux-release-x86_64OK186
macos-release-arm64OK106
macos-oldrel-arm64OK117
windows-develOK135
windows-releaseOK124
windows-oldrelOK123
wasm-releaseOK141

Exports:getDiffRhythmStatsgetExpectedMeasgetExpectedMeasIntervalsgetModelFitgetPosteriorFitgetPosteriorSamplesgetRhythmStatsgetStatsIntervalsmergeMeasMeta

Dependencies:abindashrassertthatbackportsBHBiobaseBiocGenericsBiocParallelcheckmateclicodetoolscpp11data.tableDelayedArrayDESeq2etrunctfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableHDIntervalinvgammaIRangesirlbaisobanditeratorslabelinglambda.rlatticelifecyclelimmalocfitmashrMatrixMatrixGenericsmatrixStatsmixsqpmvtnormpbsplyrR6RColorBrewerRcppRcppArmadilloRcppGSLrlangrmetaS4ArraysS4VectorsS7scalesSeqinfosnowsoftImputeSparseArraySQUAREMstatmodSummarizedExperimenttruncnormvctrsviridisLitewithrXVectorzeallot

Quantifying differential rhythmicity between conditions
Introduction | Load packages | Load the data | Fit linear models and compute posterior fits | Get rhythm statistics | Get differential rhythm statistics | Get observed and fitted time-courses
Rendered fromdifferential-rhythmicity.Rmdusingknitr::rmarkdown

Last update: 2026-01-20
Started: 2021-07-19

Quantifying rhythmicity in one condition
Introduction | Load packages | Load the data | Fit linear models | Get posterior fits | Get rhythm statistics | Get observed and fitted time-courses
Rendered fromrhythmicity.Rmdusingknitr::rmarkdown

Last update: 2026-01-20
Started: 2021-07-19

Quantifying uncertainty in (differential) rhythmicity
Introduction | Load packages | Load the data | Fit linear models and compute posterior fits | Draw samples from the posterior fits | Get fitted time-courses | Get rhythm and differential rhythm statistics
Rendered fromuncertainty.Rmdusingknitr::rmarkdown

Last update: 2026-01-20
Started: 2021-07-19

Analyzing RNA-seq data
Introduction | Load the data | Filter out lowly expressed genes | Fill in counts for sample-gene pairs having zero counts | Option 1: limma-voom | Option 2: DESeq2 | Continue using limorhyde2
Rendered fromrnaseq.Rmdusingknitr::rmarkdown

Last update: 2022-04-11
Started: 2022-01-27