| AllEqual | Check if all values in a vector are the same |
| build.best.random.forest | Try different mtry and select the best fitted model |
| build.coxregression.model | Build cox regression model |
| build.elastic.net.regression | Build elastic net regression |
| buildEnsembleModel | Build ensemble model based on h2o platform |
| buildGRangesObj | Build Genomic Ranges from data.frame |
| build.lassoOrRidge.regression | Build lasso or ridge regression |
| build.logistic.model | Build a logistic model |
| build.psm.regression.model | Build parametric survival model |
| build.randomforest.model | Build a random forests model |
| build.SVM | Build Support Vector Machines |
| cal_cnvScore | Cal_CNV score |
| calculateNMI | Ranks each features by NMI (normalized mutual information)... |
| celline_drug_group_auc_analysis | Analyze if a durg sensitivity is correlated with... |
| celline_drug_target_auc_analysis | Analyze if gene is correlated with drug sensitivity |
| cellline_drug_gene_correlation | Drug and gene correlation analysis |
| ChAMP_QC_Pipeline_Frome_Beta_Value | ChAMP QC Pipeline for beta matrix |
| check_diff_gene | Check gene expression |
| checkHousekeepingCombination | Iterate all the combination of housekeeping genes |
| clincial_impact | Plot clinical impact: detail number of patients |
| ClusterProfiler.GSEA | Perform GSEA analysis by cluster profiler |
| ClusterProfiler.GSEA.Compare | Perform GSE analysis across multiple group by cluster... |
| ClusterProfiler.GSEA.ORA.customGS | Perform analysis using user custom gene sets |
| ClusterProfiler.GSEA.ORA.customGS.Compare | Perform GSE analysis across multiple group by cluster... |
| ClusterProfiler.OverRepresentationTest | Perform over-representation test by cluster profiler |
| ClusterProfiler.OverRepresentationTest.Compare | Perform over-representation test across multiple group by... |
| compare_differential.analysis | Perform differential analysis (1 vs others) |
| compare_differential.ttest.analysis | Perform differential analysis (1 vs others) by t test |
| compare_GSE.HTSAnalyzer | Perform GSEA across multiple groups (1 vs other) |
| compareROC | Compare two ROC curves |
| confidence_interval | confidence interval |
| confusion_matrix | Get confusion matrix |
| consensusSubtyping | Identification of consensus subtypes |
| convertDfToNumeric | Convert data frame to numeric |
| convertEnsemblDF2SymbolDF | Convert Ensembl data frame to gene symbol dataframe |
| CorrelationHeatmapTwoDf | Perform correlation analysis between two data.frame |
| CorrelationHeatmapTwoDfMantelTest | Perform correlation analysis between two data.frame |
| countClassByColumn | Count the class by each column |
| count_to_tpm | Convert count to TPM |
| cross.validation | k fold n times cross validation |
| dataframe2gct_file | Convert data frame to GenePattern gct file |
| decisionCurveAnalysis | Decision curve analysis. Similar with plot.ntbft |
| decisionCurveAnalysisSimple | Decision curve analysis using risk probability and label |
| decisionCurve.diff.pvalue | Comparing two decision curves and reporting P value |
| DESeq2_differential | Differential analysis by DESEQ2 |
| determineClusterNumber | Determine the best cluster numbers |
| dimPlotWithCountBar | Plot dim plot and cell count bar |
| download.geo.dataset | Download dataset from GEO by accession ID and platform |
| draw_confusion_matrix | Confusion matrix visulization |
| draw.expression.dotplot | Draw expression by dotplot Need to be update |
| draw.mutation.type | Count each event type and draw pie chart |
| draw.mutation.type.barplot | Draw bar plot |
| drawScatter | Draw scatter plot |
| draw.target.coverage.plot | Draw target coverage plot |
| ELMER_RNA_Met_analysis | RNA and methylation analysis |
| ensembl_EntrezID | Title |
| export2ppt | Export figure to PPT https://github.com/tomwenseleers/export |
| exportScenicLoom | Export seurat object for SCENIC analysis |
| exportTable | Overwrite write.table with modified default option. Export... |
| extractSignaturePercent | Estimate signature percents |
| extractTCGASampleType | Extract TCGA sample types |
| feature.selection.4givenMLAlgorithm | Variable Importance from a specific Machine Learning... |
| feature.selection.boruta | Feature selection by Boruta |
| feature.selection.RFE | Recursive feature elimnation |
| fillNADataframe | Fill NA by row or column |
| fillSymmetricNATable | Fill NA in symmetric table |
| filterGenes | Filter genes by kinks of criteria |
| Find_doublet | Find doublet |
| findMaxMinColumnNamesForEachRow | Find the column name of maximum/minimum value for each row |
| findRepeatedGenes | Return a vector indicate gene overlapping count |
| findSomaticSignature | Identify signature from sample data |
| findSurvivalCutPoint | Determine the Optimal Cutpoint for Continuous Variables |
| forest_plot | Forest plot |
| formatTable | Format by digit |
| fpkm2tpm | Convert FPKM data fram to TPM |
| gapStat | Gap statistics |
| generateCombinations | Gnenerate combinations with specified size |
| generateGenePairValueDf | Generate gene pair value data.frame |
| generatePairValue | Generate gene pair value |
| generate.sequencial.color | Generate sequencial color |
| genereateLabelsByGroup | Generate label based on group |
| get_all_performance_table | Return a table including all metrics across different... |
| get.all.point.ROC | Get all point if you want to draw yourself |
| get.AUC | Obtain AUC value |
| getFastaSummary | Obtain sequence length from fasta file |
| get_full_mapping_table | Retrieve full ID mapping table |
| getGeneRelatedTranscripts.Gff | Retrieve all transcripts related to target genes from gtf/gff... |
| get.ggsci.color | Get colors by ggsci |
| get_individual_candidates_performance | Get individual_candidates_performance |
| get.mostDistint.color.palette | Generate a most distinctive color palatte |
| getOneRoundCVRes | Get one round CV result |
| get.palette.color | Use ggpubr function to get all kinds of color palette |
| get_performance | Get model performace, sensitivity, sepcificity and others |
| getProgramName | Get current running program name |
| getPromoterRegions | Get promoters by GenomicFeatures package. Region needed |
| get.TCGA.miRNAExpression | Get TCGA miRNA expression data |
| get.TCGA.Project.Clinical | Get TCGA project clinical information |
| get.TCGA.RNA.FPKM | Get TCGA RNA expression (RPKM) data |
| get.TCGA.sample.project.infomap | Get sample barcode and TCGA project map information |
| getTranscriptLength | Obtain transcript length from gff file or GRanges object |
| getTranscriptProteinSequence | Retrieve protein sequence by biomaRt |
| get.YoudenIndex | Get Youden index value |
| group2class_file | Convert a vector to GenePattern class file |
| groupCorrelation | Correlation plot based on average expression |
| heatmap.annotation | Only draw annotation |
| heatmap.with.lgfold.riskpro | Plot heatmap with log 2 fold change and risk probability... |
| heatmap.with.wordcloud | Plot heatmap while perform word cloud analysis |
| hello | Prints 'Hello, world!'. |
| HosmerLemesGoodnessOfFitTest | Hosmer-Lemeshow Goodness of Fit (GOF) Test |
| hyperGeoTest | Perform hypergeometric test |
| hyperGeoTest4ContingencyTable | Hyper geometrix test for contigency table |
| identifySubtypeFromMatrix | A matrix |
| id_mapping | Title |
| iflog2 | If perform log2 transformation |
| is.nan.data.frame | Generic is.nan function |
| lasso_best_lamda | Get best lamda by perform multiple round lasso-sv... |
| lasso.cox.selection | LASSO Cox selection |
| lasso.cv.select.feature | Perform multiple round lasso to select stable feature |
| lasso.select.feature | Feature selection by lasso |
| limma_differential | Differential analysis by LIMMA |
| limma.differential.cv.selection | Perform multiple rounds differential analysis to select... |
| load10X | Read data: raw to PCA |
| loadArrayExpressDataset | Download dataset from ArrayExpress |
| loadGff | Convert gff file to data frame |
| load.gmt | Read in gene set information from .gmt files |
| loadICGC.exp | clean ICGC expression matrix file |
| loadICGC.methy | clean ICGC methylation data file |
| loadMethylationArraryData | Load methylation arrary from directory |
| load.rsem.matrix | Load quantification result from RSEM by tximport |
| load.salmon.matrix | Read Salmon output |
| log2dfQuantileNormalization | Quantile normalization for log2 data frame |
| logit2prob | Convert logti to probability |
| loo.cv | Leave one out cross validation |
| loo.cv.cox | Leave one out cross validation for cox regression |
| maf2binaryTable | Convert MAF format to a binary matrix |
| MannWhitneyU_WilcoxonRankSumTest_differential | Calculate p value by MannWhitneyU (WilcoxonRankSum) Test... |
| MA_plot | M-A plot |
| meltDataFrameByGroup | Melt data frame by group |
| microarray_limma_differential | GEO dataset analysis by limma. |
| miRBaseConverter | miRBase convert |
| multiIntersection | Multiple intersction |
| multipleHyperGeoTest | Multiple hyper geomatrix test, include 2xn, 2x2 |
| multiplePlotPredictedPro | plot predictive probability distribution |
| multi_roc_with_ci | Plot multiple ROCs in one figure |
| multivariate_cox | Title |
| multivariate_or | Variate logistic analysis Row: sample, Column: gene... |
| nomogram.plot | Nomogram plot by rms |
| normalize_miRNACount_toCPM | Normalize miRNA counts to CPM |
| norm_find_scale | NormalizeData -> FindVariableFeatures -> ScaleData |
| ntbft | Net benifit |
| ntbft.boot | Net benefit Bootstrap method to correct overfitting |
| oncoPredict | Calculate drug sensitivity based on oncoPredict |
| oneway.anova | Kruskal Wallis Test One Way Anova by Ranks or F test |
| pairwiseAdonisTest | pairwiseAdonis |
| plotClevelandDot | Draw Celventland dot plot |
| plotJitterBoxplot | Boxplot with jitter, barplot with mean_se, violin plot with... |
| plot_miRCorrelation | Plot miR's correlation |
| plot.ntbft | Plotting the Net benefit function. Coule be multiple curves |
| plotPCA | PCA plot Please note: scale will be performed autmaticly |
| plotPie | Count each event type and draw pie chart |
| plotSilhouette | Silhouette plot |
| plotUpset | Upset plot |
| plotVenn | Plot venn diagram by ggvenn |
| plotVennLegacy | Plot venn diagram |
| plot_waterfall | Waterfall plot |
| pre_pseudotime_matrix | Pseudo differential analysis |
| prob2logit | Convert Probability to Logit |
| pseudoHeatmap | Pseudo heatmap |
| radarSpiderPlot | Radar plot (aka spider plot) |
| randomOrderWithinGroup | Randomly place the sample within group |
| rangeScale01 | Scale the value to 0-1 |
| readICGCExpFile | Format ICGC dataframe |
| read_mirdeep2_result | Load miRDeep2 expression matrix |
| read_mirdeep2_resultDir | Load miRDeep2 expression from a directory |
| reduce_join_list | Join a table list |
| refSeq_Ensembl | Convert RefSeq ID to Ensembl ID by biomaRt |
| removeBatchEffect | SVA combatc remove batch effect |
| remove.verylong.isoform.gff | Remove isforms with extremly long interval (isoform.End -... |
| return_immune_genes | Immune related gene |
| riskCalibrationPlot | riskCalibrationPlot |
| riskCalibrationPlot.default | Calibration plot |
| riskCalibrationPlot.lrm | Calibration plot by rms.calibrate |
| riskCalibrationPlotMultiple | Plot multiple calibration plot by riskRegression |
| riskCalibrationPlotSingleComplex | Calibration plot |
| rms_validate | Resampling Validation of a Fitted Model's Indexes of Fit |
| roc_with_ci | plot ROC with CI. Stratified bootstrap 2000 times |
| RTN.analysis | RTN Reconstruction of Transcriptional regulatory Networks... |
| RTN.network.plot | Plot RTN network |
| run_cellChat | Run cellchat |
| runCopyKAT | CopyKAT |
| runCytoTrace1 | Run cytoTRACE 1 |
| runCytoTrace2 | Run cytoTRACE 2 |
| runEPIC | run EPIC |
| runEstimate | Run estiamte |
| runImmunedeconv | Run Immunedeconv |
| runInferCNV | Run inferCNV |
| runMetaFlux | Run metaflux pipeline |
| runSlingshot | Run pesudo analysis |
| run_SNF | Run similarity network fusion |
| runWGCNA | WGCNA, Weighted correlation network analysis |
| scaleDF | Scale a data.frame by column or row |
| scenicHeatmap | AUC heatmap for scenic |
| SCT_Harmony_cluster | SCTranform HarmonyIntegration FindCluster |
| scViolinPlot | Similar to dotplot, use violin plot |
| Seurat2Monocle3 | convert seurat to monocle 3 obj |
| show_hcluster | Perform hclustering analysis |
| simplifyEnrichment | GO annotation with word cloud |
| SNF_Similairity_Hist | Similairity count |
| splitCharacter | Splite vector and return the specific element |
| splitDataByGroup | split data frame by group |
| splitGroupByCutoff | Split group by various methods. Useful |
| splitSampleByGroup | Split sample by group into traning and validation set |
| ssGSEA | ssGSEA |
| subtypeAssociationAnalysis | Subtype association: Calculate Jaccard similarity coefficient... |
| suppa.event.pie | Count each event type and draw pie chart |
| suppa.get.final.table | Combine dpis, psi and tpm file together I modified the code... |
| survivaly_analysis | Survival analysis |
| surv_ROC_DCA | Time depend ROC and AUC |
| table2Figure | Convert a text table to figure |
| tanimoto_distance | Calculate tanimoto distance |
| tcgabiolinks.get.450k.methylation | Download 450K methylation data |
| tcgabiolinks.get.junction.coverage | Download junction data by TCGAbiolinks. Pls note, V2 tag and... |
| tcgabiolinks.get.RNA.expression.log2tpm | Download RAN expression by TCGAbiolinks |
| tcgaShorterBarcode | Get shorter TCGA ID |
| testCategoricalVariableFreq | Categorical variable test |
| thisPath | Get current directory path |
| time_serials_Cindex | Draw C index across times |
| ttest_differential | Calculate p value by t.test manually |
| unique_gene_expression | Title Remove redundant gene expression data, and select the... |
| univariate_cox | Univariate Cox analysis |
| univariate_cox_sthda | Univariate Cox analysis |
| univariate_or | Variate logistic analysis Row: sample, Column: gene... |
| vector.group | Group a vector into list by group |
| volcano_plot | Volcano Plot |
| whoAmI | Introduce me |
| writeGff | Write to gff file |
