Files in ProfessionalFarmer/loonR
Common function in bioinformatics analysis

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NAMESPACE

R/Biomarker.R

R/Biomart.R

R/CNV.R R/ColorRelated.R R/Common.R R/DCA.R R/Drug.R R/FeatureSelection.R R/GEO.R R/GSE.R R/Heatmap.R R/Hello.R R/ICGC.R R/IDMapping.R R/Immune.R R/MachineLearningPlatform.H2O.R R/Methylation.R R/Mutation.R R/Network.R R/RNA.R R/SNF.R R/Stats.R R/Subtyping.R R/Suppa.R R/Survival.R R/TCGA.R R/TranscriptsRelated.R R/WES.R R/miRNA.R R/qPCR.R R/scRNA.R R/submap.R README.md

_pkgdown.yml

data/BreastCancer.rda

data/CTRP.drug.annotation.rda

data/LIRI.rda

data/Subtype.matrix.rda

data/iris.rda

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loonR.Rproj

man/AllEqual.Rd man/ChAMP_QC_Pipeline_Frome_Beta_Value.Rd man/ClusterProfiler.GSEA.Compare.Rd man/ClusterProfiler.GSEA.ORA.customGS.Compare.Rd man/ClusterProfiler.GSEA.ORA.customGS.Rd man/ClusterProfiler.GSEA.Rd man/ClusterProfiler.OverRepresentationTest.Compare.Rd man/ClusterProfiler.OverRepresentationTest.Rd man/CorrelationHeatmapTwoDf.Rd man/CorrelationHeatmapTwoDfMantelTest.Rd man/DESeq2_differential.Rd man/ELMER_RNA_Met_analysis.Rd man/Find_doublet.Rd man/HosmerLemesGoodnessOfFitTest.Rd man/MA_plot.Rd man/MannWhitneyU_WilcoxonRankSumTest_differential.Rd man/RTN.analysis.Rd man/RTN.network.plot.Rd man/SCT_Harmony_cluster.Rd man/SNF_Similairity_Hist.Rd man/Seurat2Monocle3.Rd man/build.SVM.Rd man/build.best.random.forest.Rd man/build.coxregression.model.Rd man/build.elastic.net.regression.Rd man/build.lassoOrRidge.regression.Rd man/build.logistic.model.Rd man/build.psm.regression.model.Rd man/build.randomforest.model.Rd man/buildEnsembleModel.Rd man/buildGRangesObj.Rd man/cal_cnvScore.Rd man/calculateNMI.Rd man/celline_drug_group_auc_analysis.Rd man/celline_drug_target_auc_analysis.Rd man/cellline_drug_gene_correlation.Rd man/checkHousekeepingCombination.Rd man/check_diff_gene.Rd man/clincial_impact.Rd man/compareROC.Rd man/compare_GSE.HTSAnalyzer.Rd man/compare_differential.analysis.Rd man/compare_differential.ttest.analysis.Rd man/confidence_interval.Rd man/confusion_matrix.Rd man/consensusSubtyping.Rd man/convertDfToNumeric.Rd man/convertEnsemblDF2SymbolDF.Rd man/countClassByColumn.Rd man/count_to_tpm.Rd man/cross.validation.Rd man/dataframe2gct_file.Rd man/decisionCurve.diff.pvalue.Rd man/decisionCurveAnalysis.Rd man/decisionCurveAnalysisSimple.Rd man/determineClusterNumber.Rd man/dimPlotWithCountBar.Rd man/download.geo.dataset.Rd man/draw.expression.dotplot.Rd man/draw.mutation.type.Rd man/draw.mutation.type.barplot.Rd man/draw.target.coverage.plot.Rd man/drawScatter.Rd man/draw_confusion_matrix.Rd man/ensembl_EntrezID.Rd man/export2ppt.Rd 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man/getPromoterRegions.Rd man/getTranscriptLength.Rd man/getTranscriptProteinSequence.Rd man/get_all_performance_table.Rd man/get_full_mapping_table.Rd man/get_individual_candidates_performance.Rd man/get_performance.Rd man/group2class_file.Rd man/groupCorrelation.Rd man/heatmap.annotation.Rd man/heatmap.with.lgfold.riskpro.Rd man/heatmap.with.wordcloud.Rd man/hello.Rd man/hyperGeoTest.Rd man/hyperGeoTest4ContingencyTable.Rd man/id_mapping.Rd man/identifySubtypeFromMatrix.Rd man/iflog2.Rd man/is.nan.data.frame.Rd man/lasso.cox.selection.Rd man/lasso.cv.select.feature.Rd man/lasso.select.feature.Rd man/lasso_best_lamda.Rd man/limma.differential.cv.selection.Rd man/limma_differential.Rd man/load.gmt.Rd man/load.rsem.matrix.Rd man/load.salmon.matrix.Rd man/load10X.Rd man/loadArrayExpressDataset.Rd man/loadGff.Rd man/loadICGC.exp.Rd man/loadICGC.methy.Rd man/loadMethylationArraryData.Rd man/log2dfQuantileNormalization.Rd man/logit2prob.Rd man/loo.cv.Rd man/loo.cv.cox.Rd man/maf2binaryTable.Rd man/meltDataFrameByGroup.Rd man/miRBaseConverter.Rd man/microarray_limma_differential.Rd man/multiIntersection.Rd man/multi_roc_with_ci.Rd man/multipleHyperGeoTest.Rd man/multiplePlotPredictedPro.Rd man/multivariate_cox.Rd man/multivariate_or.Rd man/nomogram.plot.Rd man/norm_find_scale.Rd man/normalize_miRNACount_toCPM.Rd man/ntbft.Rd man/ntbft.boot.Rd man/oncoPredict.Rd man/oneway.anova.Rd man/pairwiseAdonisTest.Rd man/plot.ntbft.Rd man/plotClevelandDot.Rd man/plotJitterBoxplot.Rd man/plotPCA.Rd man/plotPie.Rd man/plotSilhouette.Rd man/plotUpset.Rd man/plotVenn.Rd man/plotVennLegacy.Rd man/plot_miRCorrelation.Rd man/plot_waterfall.Rd man/pre_pseudotime_matrix.Rd man/prob2logit.Rd man/pseudoHeatmap.Rd man/radarSpiderPlot.Rd man/randomOrderWithinGroup.Rd man/rangeScale01.Rd man/readICGCExpFile.Rd man/read_mirdeep2_result.Rd man/read_mirdeep2_resultDir.Rd man/reduce_join_list.Rd man/refSeq_Ensembl.Rd man/remove.verylong.isoform.gff.Rd man/removeBatchEffect.Rd man/return_immune_genes.Rd man/ridge_plot.Rd man/riskCalibrationPlot.Rd man/riskCalibrationPlot.default.Rd man/riskCalibrationPlot.lrm.Rd man/riskCalibrationPlotMultiple.Rd man/riskCalibrationPlotSingleComplex.Rd man/rms_validate.Rd man/roc_with_ci.Rd man/runCopyKAT.Rd man/runCytoTrace1.Rd man/runCytoTrace2.Rd man/runEPIC.Rd man/runEstimate.Rd man/runImmunedeconv.Rd man/runInferCNV.Rd man/runMetaFlux.Rd man/runSlingshot.Rd man/runWGCNA.Rd man/run_RCTD.Rd man/run_SNF.Rd man/run_cellChat.Rd man/run_spotlight.Rd man/scViolinPlot.Rd man/scaleDF.Rd man/scenicHeatmap.Rd man/show_hcluster.Rd man/simplifyEnrichment.Rd man/splitCharacter.Rd man/splitDataByGroup.Rd man/splitGroupByCutoff.Rd man/splitSampleByGroup.Rd man/ssGSEA.Rd man/subtypeAssociationAnalysis.Rd man/suppa.event.pie.Rd man/suppa.get.final.table.Rd man/surv_ROC_DCA.Rd man/survivaly_analysis.Rd man/table2Figure.Rd man/tanimoto_distance.Rd man/tcgaShorterBarcode.Rd man/tcgabiolinks.get.450k.methylation.Rd man/tcgabiolinks.get.RNA.expression.log2tpm.Rd man/tcgabiolinks.get.junction.coverage.Rd man/testCategoricalVariableFreq.Rd man/thisPath.Rd man/time_serials_Cindex.Rd man/ttest_differential.Rd man/unique_gene_expression.Rd man/univariate_cox.Rd man/univariate_cox_sthda.Rd man/univariate_or.Rd man/vector.group.Rd man/volcano_plot.Rd man/whoAmI.Rd man/writeGff.Rd

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ProfessionalFarmer/loonR
Common function in bioinformatics analysis

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ProfessionalFarmer/loonR Common function in bioinformatics analysis

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ProfessionalFarmer/loonR
Common function in bioinformatics analysis

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Common function in bioinformatics analysis