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:Robert M Flight [aut, cre], Hunter NB Moseley [aut]

visualizationQualityControl_0.5.1.tar.gz
visualizationQualityControl_0.5.1.zip(r-4.7-any)visualizationQualityControl_0.5.1.zip(r-4.6-any)visualizationQualityControl_0.5.1.zip(r-4.5-any)
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:

On CRAN:

Conda:

bioinformaticscorrelationquality-controlvisualization

4.82 score 11 stars 30 scripts 22 exports 56 dependencies

Last updated from:118c765fd0 (on 0.5.1). Checks:5 WARNING, 2 OK, 2 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develWARNING200
source / vignettesOK190
linux-releaseERROR166
macos-releaseWARNING127
macos-oldrelWARNING141
windows-develWARNING136
windows-releaseWARNING133
windows-oldrelERROR91
wasm-releaseOK111

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
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
Rendered fromquality_control.Rmdusingknitr::rmarkdown

Last update: 2024-02-16
Started: 2016-03-02

PCA Testing
Purpose | Data | PCA | Test PCs | Test Loadings
Rendered frompca_testing.Rmdusingknitr::rmarkdown

Last update: 2021-12-28
Started: 2020-07-24

Readme and manuals

Help Manual

Help pageTopics
calculate values from summariescalc_sd_rsd
calculate values from summaries v2calc_sd_rsd_nls
calculate F-ratiocalculate_fratio
matching featurescount_matching_features
determine outliersdetermine_outliers
keep features with percentage of non-zerosfilter_non_zero_percentage
create set of disjoint colorsgenerate_group_colors
10 sample to sample correlationsgrp_cor
grp_cor_datagrp_cor_data
grp_exp_datagrp_exp_data
10 sample meta-datagrp_info
keep features with percentage of non-missingkeep_non_missing_percentage
keep features with percentage of non-zeroskeep_non_zero_percentage
calculate median class correlationsmedian_class_correlations
calculate median correlationsmedian_correlations
fraction of outliersoutlier_fraction
cluster and reordersimilarity_reorder
reorder by sample classsimilarity_reorderbyclass
split groupssplit_groups
summarize datasummarize_data
correlate scores and outcomevisqc_cor_pca_scores
easier heatmapsvisqc_heatmap
calculate pca contributionsvisqc_score_contributions
test loadingsvisqc_test_pca_loadings
test scores and outcomevisqc_test_pca_scores