Package: evaluomeR 1.21.6

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]

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NEWS

# 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-1.21.0(bioc 3.20)evaluomeR-1.20.0(bioc 3.19)

bioconductor-package

22 exports 0.82 score 114 dependencies

Last updated 12 days agofrom:f5e2aa6a77

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

Evaluation of Bioinformatics Metrics with evaluomeR

José Antonio Bernabé-Díaz, Manuel Franco, Juana-María Vivo, Manuel Quesada-Martínez, Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis

Rendered frommanual.Rmdusingknitr::rmarkdownon Jun 29 2024.

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

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

Package: evaluomeR 1.21.6

evaluomeR: Evaluation of Bioinformatics Metrics

Evaluation of Bioinformatics Metrics with evaluomeR

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