Package: deltaccd 1.0.4

Jake Hughey

deltaccd: Quantify Rhythmic Gene Co-Expression Relative to a Reference

Infer progression of circadian rhythms in transcriptome data in which samples are not labeled with time of day and coverage of the circadian cycle may be incomplete. See Shilts et al. (2018) <doi:10.7717/peerj.4327>.

Authors:Jake Hughey [aut, cre], Elliot Outland [aut]

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manual.pdf |manual.html✨
card.svg |card.png
deltaccd/json (API)
NEWS

# Install 'deltaccd' in R:

install.packages('deltaccd', repos = c('https://hugheylab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hugheylab/deltaccd/issues

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

Datasets:

GSE19188 - Gene expression data for GSE19188.

On CRAN:

3.00 score 1 stars 4 scripts 200 downloads 5 exports 25 dependencies

Last updated from:ee634ebb27. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	127
source / vignettes	OK	164
linux-release-x86_64	OK	167
macos-release-arm64	OK	80
macos-oldrel-arm64	OK	86
windows-devel	OK	76
windows-release	OK	89
windows-oldrel	OK	83
wasm-release	OK	106

Exports:calcCCD calcDeltaCCD getRefCor plotHeatmap plotRefHeatmap

Dependencies:cli codetools cpp11 data.table digest doRNG farver foreach ggplot2 glue gtable isoband iterators labeling lifecycle R6 RColorBrewer rlang rngtools S7 scales statmod vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate clock correlation distance (CCD).	calcCCD
Calculate delta clock correlation distance.	calcDeltaCCD
Retrieve the reference correlation matrix for circadian gene co-expression.	getRefCor
Gene expression data for GSE19188.	GSE19188
Visualize gene co-expression.	plotHeatmap
Visualize the reference pattern of gene co-expression.	plotRefHeatmap