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
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visualizationQualityControl_0.5.1.tgz(r-4.4-any)visualizationQualityControl_0.5.1.tgz(r-4.3-any)
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visualizationQualityControl.pdf |visualizationQualityControl.html✨
visualizationQualityControl/json (API)
NEWS

# Install 'visualizationQualityControl' in R:
install.packages('visualizationQualityControl', repos = c('https://moseleybioinformaticslab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/moseleybioinformaticslab/visualizationqualitycontrol/issues

Datasets:

On CRAN:

bioinformaticscorrelationquality-controlvisualization

4.73 score 9 stars 30 scripts 22 exports 62 dependencies

Last updated 9 months agofrom:118c765fd0 (on 0.5.1). Checks:OK: 1 WARNING: 5 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winWARNINGNov 12 2024
R-4.5-linuxWARNINGNov 12 2024
R-4.4-winWARNINGNov 12 2024
R-4.4-macWARNINGNov 12 2024
R-4.3-winERRORNov 12 2024
R-4.3-macWARNINGNov 12 2024

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:backportsBiocGenericsbroomcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondendsortdigestdoParalleldplyrfansifarverforeachgenericsGetoptLongggplot2GlobalOptionsgluegtableIRangesisobanditeratorsknitrProgressBarlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepillarpkgconfigpngpurrrR.methodsS3R.ooR6RColorBrewerRcpprjsonrlangS4Vectorsscalesshapestringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

PCA Testing

Rendered frompca_testing.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

Quality Control Example

Robert M Flight

Rendered fromquality_control.Rmdusingknitr::rmarkdownon Nov 12 2024.

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

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