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:	0.1.0
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:	2023-01-26
DOI:	10.32614/CRAN.package.limorhyde2
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.html , limorhyde2.pdf
Vignettes:	Quantifying differential rhythmicity between conditions (source, R code) Quantifying rhythmicity in one condition (source, R code) Analyzing RNA-seq data (source, R code) Quantifying uncertainty in (differential) rhythmicity (source, R code)

Downloads:

Package source:	limorhyde2_0.1.0.tar.gz
Windows binaries:	r-devel: limorhyde2_0.1.0.zip, r-release: limorhyde2_0.1.0.zip, r-oldrel: limorhyde2_0.1.0.zip
macOS binaries:	r-release (arm64): limorhyde2_0.1.0.tgz, r-oldrel (arm64): limorhyde2_0.1.0.tgz, r-release (x86_64): limorhyde2_0.1.0.tgz, r-oldrel (x86_64): limorhyde2_0.1.0.tgz
Old sources:	limorhyde2 archive

Linking:

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