Package: evaluomeR 1.29.0

José Antonio Bernabé-Díaz

evaluomeR: Evaluation of Bioinformatics Metrics

Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.

Authors:José Antonio Bernabé-Díaz [aut, cre], Manuel Franco [aut], Juana-María Vivo [aut], Manuel Quesada-Martínez [aut], Astrid Duque-Ramos [aut], Jesualdo Tomás Fernández-Breis [aut]

evaluomeR_1.29.0.tar.gz
evaluomeR_1.29.0.zip(r-4.7)evaluomeR_1.29.0.zip(r-4.6)evaluomeR_1.29.0.zip(r-4.5)
evaluomeR_1.29.0.tgz(r-4.6-any)evaluomeR_1.29.0.tgz(r-4.5-any)
evaluomeR_1.29.0.tar.gz(r-4.7-any)evaluomeR_1.29.0.tar.gz(r-4.6-any)
evaluomeR_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
evaluomeR/json (API)

# Install 'evaluomeR' in R:

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

Bug tracker:https://github.com/neobernad/evaluomer/issues

Datasets:

bioMetrics - Dataset: Metrics for biological pathways
ontMetrics - Dataset: Structural ontology metrics
rnaMetrics - Dataset: RNA quality metrics

On BioConductor:evaluomeR-1.29.0(bioc 3.24)evaluomeR-1.28.0(bioc 3.23)

clustering classification featureextraction assessment clustering-evaluation evaluome evaluomer metrics

5.19 score 52 scripts 22 exports 102 dependencies

Last updated from:8c16ae0006. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	194
linux-devel-x86_64	WARNING	412
source / vignettes	OK	271
linux-release-x86_64	WARNING	391
macos-release-arm64	WARNING	256
macos-oldrel-arm64	WARNING	174
windows-devel	WARNING	281
windows-release	WARNING	286
windows-oldrel	WARNING	288
wasm-release	OK	178

Exports:annotateClustersByMetric clusterbootWrapper evaluomeRSupportedCBI getDataQualityRange getMetricRangeByCluster getMetricsRelevancy getOptimalKValue globalMetric metricsCorrelations plotMetricsBoxplot plotMetricsCluster plotMetricsClusterComparison plotMetricsMinMax plotMetricsViolin quality qualityRange qualitySet stability stabilityRange stabilitySet standardizeQualityData standardizeStabilityData

Dependencies:abind base64enc Biobase BiocBaseUtils BiocGenerics bslib cachem class cli cluster corrplot cpp11 DelayedArray dendextend DEoptimR digest diptest dplyr evaluate farver fastmap flexclust flexmix fontawesome fpc fs generics GenomicRanges ggdendro ggplot2 glue gridExtra gtable highr htmltools IRanges isoband jquerylib jsonlite kableExtra kernlab knitr labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime modeltools MultiAssayExperiment nnet pillar pkgconfig plotrix plyr prabclus purrr R6 randomForest rappdirs rbibutils RColorBrewer Rcpp Rdpack reshape2 rlang rmarkdown robustbase RSKC rstudioapi S4Arrays S4Vectors S7 sass scales Seqinfo sparcl SparseArray stringi stringr SummarizedExperiment svglite systemfonts textshaping tibble tidyr tidyselect tinytex utf8 vctrs viridis viridisLite withr xfun xml2 XVector yaml

Evaluation of Bioinformatics Metrics with evaluomeR

Rendered frommanual.Rmdusingknitr::rmarkdown

Last update: 2024-06-17
Started: 2019-02-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate the cluster ID from the optimal cluster per metric for each individual. annotateClustersByMetric	annotateClustersByMetric
Dataset: Metrics for biological pathways	bioMetrics
Get supported CBIs in evaluomeR.	evaluomeRSupportedCBI
Dataframe getter for 'qualityRange' function.	getDataQualityRange
Get the range of each metric per cluster from the optimal cluster. getMetricRangeByCluster	getMetricRangeByCluster
Get the range of each metric per cluster from the optimal cluster. getMetricRangeByCluster	getMetricRangeByCluster getMetricsRelevancy
Calculating the optimal value of k. getOptimalKValue	getOptimalKValue
Global metric score defined by a prediction.	globalMetric
Calculation of Pearson correlation coefficient.	metricsCorrelations
Dataset: Structural ontology metrics	ontMetrics
Metric values as a boxplot.	plotMetricsBoxplot
Metric values clustering.	plotMetricsCluster
Comparison between two clusterings as plot. plotMetricsClusterComparison	plotMetricsClusterComparison
Minimum and maximum metric values plot.	plotMetricsMinMax
Metric values as violin plot.	plotMetricsViolin
Goodness of classifications.	quality
Goodness of classifications for a range of k clusters.	qualityRange
Goodness of classifications for a set of k clusters.	qualitySet
Dataset: RNA quality metrics	rnaMetrics
Stability index.	stability
Stability index for a range of k clusters.	stabilityRange
Stability index for a set of k clusters.	stabilitySet