Introduction | Data | Data Transformation | Principal Components Analysis | Visualize Them | Correlation Heatmap | Calculate Correlations | Reorder Correlations | Color by Class | Map Correlation to Color | Heatmap! | Median Correlation | Good | Bad | Proportion of Outlier Features | Conclusion
Package: visualizationQualityControl 0.5.1
Robert M Flight
visualizationQualityControl: Development of visualization methods for quality control
Provides utilities useful quality control of high-throughput -omics datasets.
Authors:
visualizationQualityControl_0.5.1.tar.gz
visualizationQualityControl_0.5.1.zip(r-4.7)visualizationQualityControl_0.5.1.zip(r-4.6)visualizationQualityControl_0.5.1.zip(r-4.5)
visualizationQualityControl_0.5.1.tgz(r-4.6-any)visualizationQualityControl_0.5.1.tgz(r-4.5-any)
visualizationQualityControl_0.5.1.tar.gz(r-4.7-any)visualizationQualityControl_0.5.1.tar.gz(r-4.6-any)
visualizationQualityControl_0.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
visualizationQualityControl/json (API)
| # Install 'visualizationQualityControl' in R: |
| install.packages('visualizationQualityControl', repos = c('https://moseleybioinformaticslab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/moseleybioinformaticslab/visualizationqualitycontrol/issues
Pkgdown/docs site:https://moseleybioinformaticslab.github.io
Datasets:
- grp_cor - 10 sample to sample correlations
- grp_cor_data - Grp_cor_data
- grp_exp_data - Grp_exp_data
- grp_info - 10 sample meta-data
bioinformaticscorrelationquality-controlvisualization
Last updated from:118c765fd0 (on 0.5.1). Checks:6 WARNING, 2 OK, 1 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 183 | ||
| source / vignettes | OK | 215 | ||
| linux-release-x86_64 | WARNING | 179 | ||
| macos-release-arm64 | WARNING | 135 | ||
| macos-oldrel-arm64 | ERROR | 97 | ||
| windows-devel | WARNING | 122 | ||
| windows-release | WARNING | 121 | ||
| windows-oldrel | WARNING | 116 | ||
| wasm-release | OK | 118 |
Exports:%>%calc_sd_rsdcalc_sd_rsd_nlscalculate_fratiocount_matching_featuresdetermine_outliersfilter_non_zero_percentagegenerate_group_colorskeep_non_missing_percentagekeep_non_zero_percentagemedian_class_correlationsmedian_correlationsoutlier_fractionsimilarity_reordersimilarity_reorderbyclasssplit_groupssummarize_datavisqc_cor_pca_scoresvisqc_heatmapvisqc_score_contributionsvisqc_test_pca_loadingsvisqc_test_pca_scores
Dependencies:backportsBiocGenericsbroomcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondendsortdigestdoParalleldplyrfarverforeachgenericsGetoptLongggplot2GlobalOptionsgluegtableIRangesisobanditeratorsknitrProgressBarlabelinglifecyclemagrittrmatrixStatspillarpkgconfigpngpurrrR.methodsS3R.ooR6RColorBrewerRcpprjsonrlangS4VectorsS7scalesshapestringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Quality Control Example
Last update: 2024-02-16
Started: 2016-03-02
PCA Testing
Purpose | Data | PCA | Test PCs | Test Loadings
Last update: 2021-12-28
Started: 2020-07-24
