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:
deltaccd_1.0.4.tar.gz
deltaccd_1.0.4.zip(r-4.5)deltaccd_1.0.4.zip(r-4.4)deltaccd_1.0.4.zip(r-4.3)
deltaccd_1.0.4.tgz(r-4.4-any)deltaccd_1.0.4.tgz(r-4.3-any)
deltaccd_1.0.4.tar.gz(r-4.5-noble)deltaccd_1.0.4.tar.gz(r-4.4-noble)
deltaccd_1.0.4.tgz(r-4.4-emscripten)deltaccd_1.0.4.tgz(r-4.3-emscripten)
deltaccd.pdf |deltaccd.html✨
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
- GSE19188 - Gene expression data for GSE19188.
Last updated 2 years agofrom:ee634ebb27. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win | OK | Nov 20 2024 |
| R-4.5-linux | OK | Nov 20 2024 |
| R-4.4-win | OK | Nov 20 2024 |
| R-4.4-mac | OK | Nov 20 2024 |
| R-4.3-win | OK | Nov 20 2024 |
| R-4.3-mac | OK | Nov 20 2024 |
Exports:calcCCDcalcDeltaCCDgetRefCorplotHeatmapplotRefHeatmap
Dependencies:clicodetoolscolorspacedata.tabledigestdoRNGfansifarverforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangrngtoolsscalesstatmodtibbleutf8vctrsviridisLitewithr
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 |
