NEWS.md

In hugheylab/limorhyde2: Quantify Rhythmicity and Differential Rhythmicity in Genomic Data

limorhyde2 0.1.0

• Changed default for credible interval mass to 0.9.

limorhyde2 0.0.13

• Fixed getExpectedMeas() for single condition and no covariates.

limorhyde2 0.0.12

• Added isAlreadyInParallel() function that checks if you are already running something in parallel.
• Added check to getRhythmStats() to prevent running in parallel if already in parallel.

limorhyde2 0.0.11

• Fixed mergeMeasMeta() for RNA-seq data.

limorhyde2 0.0.10

• Matched styling to lab standards.

limorhyde2 0.0.9

• Enabled spline fit with fewer knots and customizable degree.

limorhyde2 0.0.8

• Matched style to lab standard.

limorhyde2 0.0.7

• Made data smaller and examples faster.

limorhyde2 0.0.6

• Switched to using updated ashr from CRAN.

limorhyde2 0.0.4

• Added more stringent checking for correspondence between measurements matrix and metadata.

limorhyde2 0.0.3

• Made mash silent.
• Added checking for parallel backend, to avoid warning messages.

limorhyde2 0.0.2

• Moved data to data/, to make examples and vignettes simpler.
• Added examples.

limorhyde2 0.0.1

• Updated vignette for analyzing RNA-seq data.

limorhyde2 0.0.0.9033

• Renamed mean_value to mesor and added differential rhythm statistics for mean mesor and mean amp.

limorhyde2 0.0.0.9032

• Added differential rhythm statistic diff_rhy_dist.

limorhyde2 0.0.0.9031

• Cleaned up calculation of credible intervals for rhythm amplitudes.

limorhyde2 0.0.0.9030

• Updated model parameterization and mashing to treat all conditions fairly.

limorhyde2 0.0.0.9029

• Updated calculation of credible intervals for rhythm amplitudes.

limorhyde2 0.0.0.9028

• Added vignette for RNA-seq data.

limorhyde2 0.0.0.9027

• Added ability to fit models using DESeq2.

limorhyde2 0.0.0.9026

• Made calculation of rms-based stats optional.
• Simplified tests to use snapshotting.

limorhyde2 0.0.0.9025

• Changed assertLogical() to assertFlag() for checking inputs.

limorhyde2 0.0.0.9024

• Fixed vignette building on Windows machines

limorhyde2 0.0.0.9023

• Fixed factor weirdness between R versions

limorhyde2 0.0.0.9022

• Output for getDiffRhythmStats() now includes all pairs of conditions by default

limorhyde2 0.0.0.9021

• Fixed bug so getDiffRhythmStats uses all shifted models

limorhyde2 0.0.0.9020

• Replaced globalVariables() with assigning variables to NULL in each function

limorhyde2 0.0.0.9019

• Clarified wording in vignettes

limorhyde2 0.0.0.9018

• Added function to merge measurements and metadata
• Added vignettes

limorhyde2 0.0.0.9017

• Fixed bug in getStatsIntervals

limorhyde2 0.0.0.9016

• Cleaned up logic around nKnots for cosinor
• Fixed setting attributes for data.tables
• Fixed input check in getDiffRhythmStats

limorhyde2 0.0.0.9015

• Revamped input checking to use the checkmate package

hugheylab/limorhyde2 documentation built on Jan. 29, 2024, 8:36 p.m.