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.

Version: 0.0.7
Depends: R (≥ 3.6)
Imports: abind (≥ 1.4-5), ashr (≥ 2.2-54), checkmate (≥ 2.0.0), data.table (≥ 1.12.8), DESeq2 (≥ 1.30.0), foreach (≥ 1.5.0), HDInterval (≥ 0.2.2), iterators (≥ 1.0.12), limma (≥ 3.42.2), mashr (≥ 0.2.50), pbs (≥ 1.1), zeallot (≥ 0.1.0)
Suggests: cowplot (≥ 1.1.1), knitr, doParallel (≥ 1.0.15), ggplot2 (≥ 3.3.5), glue (≥ 1.6.1), qs (≥ 0.24.1), rmarkdown, testthat (≥ 3.0.0)
Published: 2022-03-08
Author: Jake Hughey [aut, cre], Dora Obodo [aut], Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey at gmail.com>
License: GPL-2
URL: https://limorhyde2.hugheylab.org, https://github.com/hugheylab/limorhyde2
NeedsCompilation: no
Materials: NEWS
CRAN checks: limorhyde2 results

Documentation:

Reference manual: limorhyde2.pdf
Vignettes: Quantifying differential rhythmicity between conditions
Quantifying rhythmicity in one condition
Analyzing RNA-seq data
Quantifying uncertainty in (differential) rhythmicity

Downloads:

Package source: limorhyde2_0.0.7.tar.gz
Windows binaries: r-devel: limorhyde2_0.0.7.zip, r-release: limorhyde2_0.0.7.zip, r-oldrel: limorhyde2_0.0.7.zip
macOS binaries: r-release (arm64): limorhyde2_0.0.7.tgz, r-release (x86_64): limorhyde2_0.0.7.tgz, r-oldrel: not available

Linking:

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