Files in neobernad/evaluomeR
Evaluation of Bioinformatics Metrics
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/correlation.R
R/data.R
R/dataPreprocessing.R
R/helpers.R
R/internalClusterboot.R
R/internalFunctions.R
R/metricsAnalysis.R
R/predictions.R
R/qualityIndices.R
R/stabilityIndex.R
README.md
data/bioMetrics.RData
data/golub.RData
data/nci60_k10.RData
data/nci60_k8.RData
data/ontMetrics.RData
data/ontMetricsOBO.RData
data/rnaMetrics.RData
docs/index.html
inst/REFERENCES.bib
man/ATSC.Rd
man/PCASuitability.Rd
man/annotateClustersByMetric.Rd
man/bioMetrics.Rd
man/cleanDataset.Rd
man/determineNumberOfFactors.Rd
man/evaluomeRSupportedCBI.Rd
man/getDataQualityRange.Rd
man/getMetricRangeByCluster.Rd
man/getMetricsRelevancy.Rd
man/getOptimalKValue.Rd
man/getRSKCAlpha.Rd
man/getRSKCL1Boundry.Rd
man/globalMetric.Rd
man/metricsCorrelations.Rd
man/ontMetrics.Rd
man/performPCA.Rd
man/plotMetricsBoxplot.Rd
man/plotMetricsCluster.Rd
man/plotMetricsClusterComparison.Rd
man/plotMetricsMinMax.Rd
man/plotMetricsViolin.Rd
man/plotPCA_fviz_biplot.Rd
man/plotPCA_fviz_screeplot.Rd
man/quality.Rd
man/qualityRange.Rd
man/qualitySet.Rd
man/removeCorrelations.Rd
man/removeNonNumericColumns.Rd
man/rnaMetrics.Rd
man/stability.Rd
man/stabilityRange.Rd
man/stabilitySet.Rd
notebooks/examples/.ipynb_checkpoints/evaluomeR_RSKC_metric_relevancy-checkpoint.ipynb
notebooks/examples/.ipynb_checkpoints/evaluomeR_optimal_k_analysis-checkpoint.ipynb
notebooks/examples/data/agro.csv
notebooks/examples/evaluomeR_RSKC_metric_relevancy.ipynb
notebooks/examples/evaluomeR_optimal_k_analysis.ipynb
notebooks/local/NCI60-cbis.ipynb
notebooks/local/NCI60.ipynb
notebooks/local/evaluomeR-RSKC.ipynb
notebooks/local/evaluomeR-Step_0.ipynb
notebooks/local/evaluomeR-Step_1.ipynb
notebooks/local/evaluomeR-Step_3_alpha.ipynb
notebooks/local/evaluomeR-autoRSKC.ipynb
notebooks/local/evaluomeR-run1.ipynb
notebooks/local/golub-cbis.ipynb
notebooks/local/golub-rskc.ipynb
notebooks/local/golub.ipynb
notebooks/local/k3clara_k4kmeans.xlsx
notebooks/local/k_opt.xlsx
notebooks/local/leukemia.RData
notebooks/local/sensitivity_cer.xlsx
notebooks/use_cases/.ipynb_checkpoints/NCI60-atsc-clara-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/NCI60-atsc-gold-standard-clara-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/NCI60-atsc-gold-standard-kmeans-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/NCI60-atsc-kmeans-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/NCI60-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/NCI60-clest-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/NCI60-clusterAnalysis-clest-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/NCI60-rskc-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/former_NCI60-rskc-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/former_golub-clest-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/former_golub-rskc-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/former_nci60-clest-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/golub-atsc-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/golub-atsc-gold-standard-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/golub-cbis-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/golub-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/golub-clest-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/golub-clusterAnalysis-clest-checkpoint.ipynb
notebooks/use_cases/.ipynb_checkpoints/golub-rskc-checkpoint.ipynb
notebooks/use_cases/NCI60-atsc-clara.ipynb
notebooks/use_cases/NCI60-atsc-gold-standard-clara.ipynb
notebooks/use_cases/NCI60-atsc-gold-standard-kmeans.ipynb
notebooks/use_cases/NCI60-atsc-kmeans.ipynb
notebooks/use_cases/NCI60-clest.ipynb
notebooks/use_cases/NCI60-clusterAnalysis-clest.ipynb
notebooks/use_cases/NCI60-rskc.ipynb
notebooks/use_cases/NCI60.ipynb
notebooks/use_cases/data/leukemia.RData
notebooks/use_cases/former_NCI60-clest.ipynb
notebooks/use_cases/former_NCI60-rskc.ipynb
notebooks/use_cases/former_golub-clest.ipynb
notebooks/use_cases/former_golub-rskc.ipynb
notebooks/use_cases/golub-atsc-gold-standard.ipynb
notebooks/use_cases/golub-atsc.ipynb
notebooks/use_cases/golub-clest.ipynb
notebooks/use_cases/golub-clusterAnalysis-clest.ipynb
notebooks/use_cases/golub-rskc.ipynb
notebooks/use_cases/golub.ipynb
tests/testATSC.R
tests/testATSC_GoldStandard.R
tests/testAll.R
tests/testAnalysis.R
tests/testCBI.R
tests/testDataPreprocessing.R
tests/testMetricsRelevancy.R
tests/testQuality.R
tests/testStability.R
usecases/kcomparison/agro.R
usecases/kcomparison/data/agro.csv
usecases/kcomparison/data/obo-119.csv
usecases/kcomparison/functions.R
usecases/kcomparison/main.R
usecases/kcomparison/mainCBI.R
usecases/kcomparison/obo.R
usecases/kcomparison/results-agro/agro.goodness.csv
usecases/kcomparison/results-agro/agro.optimal.k.csv
usecases/kcomparison/results-agro/agro.stability.csv
usecases/kcomparison/results-agro/clusters/agro.optimal.k.xlsx
usecases/kcomparison/results-agro/clusters/agro.optimal.k_clara.csv
usecases/kcomparison/results-agro/clusters/agro.optimal.k_clara_pam.csv
usecases/kcomparison/results-agro/clusters/agro.optimal.k_hclust.csv
usecases/kcomparison/results-agro/clusters/agro.optimal.k_kmeans.csv
usecases/kcomparison/results-agro/clusters/agro.optimal.k_pamk.csv
usecases/kcomparison/results-agro/clusters/agro.optimal.k_pamk_pam.csv
usecases/kcomparison/results-cbi/data.RData
usecases/kcomparison/results-cbi/kopt_table_cuanlitative_clara.csv
usecases/kcomparison/results-cbi/kopt_table_cuanlitative_kmeans.csv
usecases/kcomparison/results-cbi/kopt_table_cuanlitative_pam.csv
usecases/kcomparison/results-cbi/optimal_ks_for_cbi_repo.png
usecases/kcomparison/results-k/agro_CBOOnto_3.png
usecases/kcomparison/results-k/agro_RFCOnto_3.png
usecases/kcomparison/results-k/agro_scaled_raw_scores_kopt_k5.png
usecases/kcomparison/results-k/both_repo_k_values.csv
usecases/kcomparison/results-k/both_repo_k_values_cualitative.csv
usecases/kcomparison/results-k/kopt.eps
usecases/kcomparison/results-k/kopt.png
usecases/kcomparison/results-k/kopt_vs_k=5.eps
usecases/kcomparison/results-k/kopt_vs_k=5.png
usecases/kcomparison/results-k/obo_CBOOnto_3.png
usecases/kcomparison/results-k/obo_RFCOnto_3.png
usecases/kcomparison/results-k/obo_scaled_raw_scores_kopt_k5.png
usecases/kcomparison/results-k/stability_qualityKopt.csv
usecases/kcomparison/results-k/table_clara.csv
usecases/kcomparison/results-k/table_clara_pam.csv
usecases/kcomparison/results-k/table_kmeans.csv
usecases/kcomparison/results-k/table_pamk.csv
usecases/kcomparison/results-k/table_pamk_pam.csv
usecases/kcomparison/results-obo/clusters/obo.optimal.k.xlsx
usecases/kcomparison/results-obo/clusters/obo.optimal.k_clara.csv
usecases/kcomparison/results-obo/clusters/obo.optimal.k_clara_pam.csv
usecases/kcomparison/results-obo/clusters/obo.optimal.k_hclust.csv
usecases/kcomparison/results-obo/clusters/obo.optimal.k_kmeans.csv
usecases/kcomparison/results-obo/clusters/obo.optimal.k_pamk.csv
usecases/kcomparison/results-obo/clusters/obo.optimal.k_pamk_pam.csv
usecases/kcomparison/results-obo/obo.goodness.csv
usecases/kcomparison/results-obo/obo.optimal.k.csv
usecases/kcomparison/results-obo/obo.stability.csv
usecases/usecase1-old/analysis-matcomp.R
usecases/usecase1-old/analysis-multi.R
usecases/usecase1-old/analysis-multimc.R
usecases/usecase1-old/data/data-matcomp15.csv
usecases/usecase1-old/data/data-matcomp16.csv
usecases/usecase1-old/data/data-matcomp17.csv
usecases/usecase1-old/data/data-multi15.csv
usecases/usecase1-old/data/data-multi16.csv
usecases/usecase1-old/data/data-multi17.csv
usecases/usecase1-old/data/data-multimc15.csv
usecases/usecase1-old/data/data-multimc16.csv
usecases/usecase1-old/data/data-multimc17.csv
usecases/usecase1-old/results-matcomp/mc15_GlobalStability.png
usecases/usecase1-old/results-matcomp/mc15_QualityIndices.png
usecases/usecase1-old/results-matcomp/mc16_GlobalStability.png
usecases/usecase1-old/results-matcomp/mc16_QualityIndices.png
usecases/usecase1-old/results-matcomp/mc17_GlobalStability.png
usecases/usecase1-old/results-matcomp/mc17_QualityIndices.png
usecases/usecase1-old/results-matcomp/qualitymc15.csv
usecases/usecase1-old/results-matcomp/qualitymc16.csv
usecases/usecase1-old/results-matcomp/qualitymc17.csv
usecases/usecase1-old/results-matcomp/stabilitymc15.csv
usecases/usecase1-old/results-matcomp/stabilitymc16.csv
usecases/usecase1-old/results-matcomp/stabilitymc17.csv
usecases/usecase1-old/results-multi/multi15_GlobalStability.png
usecases/usecase1-old/results-multi/multi15_QualityIndices.png
usecases/usecase1-old/results-multi/multi16_GlobalStability.png
usecases/usecase1-old/results-multi/multi16_QualityIndices.png
usecases/usecase1-old/results-multi/multi17_GlobalStability.png
usecases/usecase1-old/results-multi/multi17_QualityIndices.png
usecases/usecase1-old/results-multi/qualitymulti15.csv
usecases/usecase1-old/results-multi/qualitymulti16.csv
usecases/usecase1-old/results-multi/qualitymulti17.csv
usecases/usecase1-old/results-multi/stabilitymulti15.csv
usecases/usecase1-old/results-multi/stabilitymulti16.csv
usecases/usecase1-old/results-multi/stabilitymulti17.csv
usecases/usecase1-old/results-multimc/multimc15_GlobalStability.png
usecases/usecase1-old/results-multimc/multimc15_QualityIndices.png
usecases/usecase1-old/results-multimc/multimc16_GlobalStability.png
usecases/usecase1-old/results-multimc/multimc16_QualityIndices.png
usecases/usecase1-old/results-multimc/multimc17_GlobalStability.png
usecases/usecase1-old/results-multimc/multimc17_QualityIndices.png
usecases/usecase1-old/results-multimc/qualitymultimc15.csv
usecases/usecase1-old/results-multimc/qualitymultimc16.csv
usecases/usecase1-old/results-multimc/qualitymultimc17.csv
usecases/usecase1-old/results-multimc/stabilitymultimc15.csv
usecases/usecase1-old/results-multimc/stabilitymultimc16.csv
usecases/usecase1-old/results-multimc/stabilitymultimc17.csv
usecases/usecase1-rsm/data/data-matcomp15.csv
usecases/usecase1-rsm/data/data-matcomp16.csv
usecases/usecase1-rsm/data/data-matcomp17.csv
usecases/usecase1-rsm/data/data-multi15.csv
usecases/usecase1-rsm/data/data-multi16.csv
usecases/usecase1-rsm/data/data-multi17.csv
usecases/usecase1-rsm/data/data-multimc15.csv
usecases/usecase1-rsm/data/data-multimc16.csv
usecases/usecase1-rsm/data/data-multimc17.csv
usecases/usecase1-rsm/plots/silhouette_impact_factor.pdf
usecases/usecase1-rsm/plots/stability_impact_factor.pdf
usecases/usecase1-rsm/plots/stability_silhouette_impact_factor.pdf
usecases/usecase1-rsm/plots/stability_silhouette_impact_factor.tiff
usecases/usecase1-rsm/results-csv/qualityMatcomp15.csv
usecases/usecase1-rsm/results-csv/qualityMatcomp16.csv
usecases/usecase1-rsm/results-csv/qualityMatcomp17.csv
usecases/usecase1-rsm/results-csv/qualityMulti15.csv
usecases/usecase1-rsm/results-csv/qualityMulti16.csv
usecases/usecase1-rsm/results-csv/qualityMulti17.csv
usecases/usecase1-rsm/results-csv/qualityMultimc15.csv
usecases/usecase1-rsm/results-csv/qualityMultimc16.csv
usecases/usecase1-rsm/results-csv/qualityMultimc17.csv
usecases/usecase1-rsm/results-csv/stabilityMatcomp15.csv
usecases/usecase1-rsm/results-csv/stabilityMatcomp16.csv
usecases/usecase1-rsm/results-csv/stabilityMatcomp17.csv
usecases/usecase1-rsm/results-csv/stabilityMulti15.csv
usecases/usecase1-rsm/results-csv/stabilityMulti16.csv
usecases/usecase1-rsm/results-csv/stabilityMulti17.csv
usecases/usecase1-rsm/results-csv/stabilityMultimc15.csv
usecases/usecase1-rsm/results-csv/stabilityMultimc16.csv
usecases/usecase1-rsm/results-csv/stabilityMultimc17.csv
usecases/usecase1-rsm/run.R
usecases/usecase1/data/data-csai15.csv
usecases/usecase1/data/data-csai16.csv
usecases/usecase1/data/data-csai17.csv
usecases/usecase1/data/data-csai18.csv
usecases/usecase1/data/data-csai19.csv
usecases/usecase1/data/data-csai20.csv
usecases/usecase1/data/data-csis15.csv
usecases/usecase1/data/data-csis16.csv
usecases/usecase1/data/data-csis17.csv
usecases/usecase1/data/data-csis18.csv
usecases/usecase1/data/data-csis19.csv
usecases/usecase1/data/data-csis20.csv
usecases/usecase1/data/data-orms15.csv
usecases/usecase1/data/data-orms16.csv
usecases/usecase1/data/data-orms17.csv
usecases/usecase1/data/data-orms18.csv
usecases/usecase1/data/data-orms19.csv
usecases/usecase1/data/data-orms20.csv
usecases/usecase1/plots/silhouette_impact_factor.pdf
usecases/usecase1/plots/silhouette_impact_factor_by_year.pdf
usecases/usecase1/plots/stability_impact_factor.pdf
usecases/usecase1/plots/stability_impact_factor_by_year.pdf
usecases/usecase1/plots/stability_silhouette_impact_factor.pdf
usecases/usecase1/plots/stability_silhouette_impact_factor_by_year.pdf
usecases/usecase1/results-csv/qualityCsai16.csv
usecases/usecase1/results-csv/qualityCsai17.csv
usecases/usecase1/results-csv/qualityCsai18.csv
usecases/usecase1/results-csv/qualityCsai19.csv
usecases/usecase1/results-csv/qualityCsai20.csv
usecases/usecase1/results-csv/qualityCsis16.csv
usecases/usecase1/results-csv/qualityCsis17.csv
usecases/usecase1/results-csv/qualityCsis18.csv
usecases/usecase1/results-csv/qualityCsis19.csv
usecases/usecase1/results-csv/qualityCsis20.csv
usecases/usecase1/results-csv/qualityOrms16.csv
usecases/usecase1/results-csv/qualityOrms17.csv
usecases/usecase1/results-csv/qualityOrms18.csv
usecases/usecase1/results-csv/qualityOrms19.csv
usecases/usecase1/results-csv/qualityOrms20.csv
usecases/usecase1/results-csv/stabilityCsai16.csv
usecases/usecase1/results-csv/stabilityCsai17.csv
usecases/usecase1/results-csv/stabilityCsai18.csv
usecases/usecase1/results-csv/stabilityCsai19.csv
usecases/usecase1/results-csv/stabilityCsai20.csv
usecases/usecase1/results-csv/stabilityCsis16.csv
usecases/usecase1/results-csv/stabilityCsis17.csv
usecases/usecase1/results-csv/stabilityCsis18.csv
usecases/usecase1/results-csv/stabilityCsis19.csv
usecases/usecase1/results-csv/stabilityCsis20.csv
usecases/usecase1/results-csv/stabilityOrms16.csv
usecases/usecase1/results-csv/stabilityOrms17.csv
usecases/usecase1/results-csv/stabilityOrms18.csv
usecases/usecase1/results-csv/stabilityOrms19.csv
usecases/usecase1/results-csv/stabilityOrms20.csv
usecases/usecase1/run.R
usecases/usecase2-old/analysis-agro-obo.R
usecases/usecase2-old/analysis-agro.R
usecases/usecase2-old/analysis-obo.R
usecases/usecase2-old/data/agro.csv
usecases/usecase2-old/data/obo-119.csv
usecases/usecase2-old/optimal-k.R
usecases/usecase2-old/results-agro-obo/agro_obo.correlation.csv
usecases/usecase2-old/results-agro-obo/correlation.png
usecases/usecase2-old/results-agro-obo/quality_k=2.csv
usecases/usecase2-old/results-agro-obo/quality_k=3.csv
usecases/usecase2-old/results-agro-obo/quality_k=4.csv
usecases/usecase2-old/results-agro-obo/quality_k=5.csv
usecases/usecase2-old/results-agro-obo/quality_k=6.csv
usecases/usecase2-old/results-agro-obo/quality_k_2_6.png
usecases/usecase2-old/results-agro-obo/stability.csv
usecases/usecase2-old/results-agro-obo/stability_k_2_6.png
usecases/usecase2-old/results-agro/agro.correlation.csv
usecases/usecase2-old/results-agro/correlation.png
usecases/usecase2-old/results-agro/quality_k_2_6.png
usecases/usecase2-old/results-agro/stability.csv
usecases/usecase2-old/results-agro/stability_k=2.csv
usecases/usecase2-old/results-agro/stability_k=3.csv
usecases/usecase2-old/results-agro/stability_k=4.csv
usecases/usecase2-old/results-agro/stability_k=5.csv
usecases/usecase2-old/results-agro/stability_k=6.csv
usecases/usecase2-old/results-agro/stability_k_2_6.png
usecases/usecase2-old/results-obo/correlation.png
usecases/usecase2-old/results-obo/obo.correlation.csv
usecases/usecase2-old/results-obo/quality_k_2_6.png
usecases/usecase2-old/results-obo/stability.csv
usecases/usecase2-old/results-obo/stability_k=2.csv
usecases/usecase2-old/results-obo/stability_k=3.csv
usecases/usecase2-old/results-obo/stability_k=4.csv
usecases/usecase2-old/results-obo/stability_k=5.csv
usecases/usecase2-old/results-obo/stability_k=6.csv
usecases/usecase2-old/results-obo/stability_k_2_6.png
usecases/usecase2/data/agro.csv
usecases/usecase2/data/obo-119.csv
usecases/usecase2/plots/silhouette_agro_obo_both.pdf
usecases/usecase2/plots/stability_agro_obo_both.pdf
usecases/usecase2/plots/stability_silhouette_agro_obo_both.pdf
usecases/usecase2/plots/stability_silhouette_agro_obo_both.tiff
usecases/usecase2/results-csv/qualityAgro.csv
usecases/usecase2/results-csv/qualityAgro_Obo.csv
usecases/usecase2/results-csv/qualityObo.csv
usecases/usecase2/results-csv/stabilityAgro.csv
usecases/usecase2/results-csv/stabilityAgro_Obo.csv
usecases/usecase2/results-csv/stabilityObo.csv
usecases/usecase2/run.R
usecases/usecase3/data/bangertdrowns2004.csv
usecases/usecase3/data/li2007.csv
usecases/usecase3/data/molloy2014.csv
usecases/usecase3/plots/forest_bangertdrowns2004_grade_cluster_SMD.pdf
usecases/usecase3/plots/forest_li2007_cluster_OR.pdf
usecases/usecase3/plots/forest_molloy2014_quality_cluster_ZCOR.pdf
usecases/usecase3/plots/silhouette_metafor.pdf
usecases/usecase3/plots/stability_metafor.pdf
usecases/usecase3/plots/stability_silhouette_metafor.pdf
usecases/usecase3/plots/stability_silhouette_metafor.tiff
usecases/usecase3/results-csv/qualityBangert.csv
usecases/usecase3/results-csv/qualityLi.csv
usecases/usecase3/results-csv/qualityMolloy.csv
usecases/usecase3/results-csv/stabilityBangert.csv
usecases/usecase3/results-csv/stabilityLi.csv
usecases/usecase3/results-csv/stabilityMolloy.csv
usecases/usecase3/run.R
vignettes/manual.Rmd
