ProfessionalFarmer/loonR
Common function in bioinformatics analysis

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ProfessionalFarmer/loonR: Common function in bioinformatics analysis
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API

API for ProfessionalFarmer/loonR
Common function in bioinformatics analysis

Global functions
AllEqual Man page Source code
ChAMP_QC_Pipeline_Frome_Beta_Value Man page Source code
ClusterProfiler.GSEA Man page Source code
ClusterProfiler.GSEA.Compare Man page Source code
ClusterProfiler.GSEA.ORA.customGS Man page Source code
ClusterProfiler.GSEA.ORA.customGS.Compare Man page Source code
ClusterProfiler.OverRepresentationTest Man page Source code
ClusterProfiler.OverRepresentationTest.Compare Man page Source code
CorrelationHeatmapTwoDf Man page Source code
CorrelationHeatmapTwoDfMantelTest Man page Source code
DESeq2_differential Man page Source code
ELMER_RNA_Met_analysis Man page Source code
Find_doublet Man page Source code
HosmerLemesGoodnessOfFitTest Man page Source code
MA_plot Man page Source code
MannWhitneyU_WilcoxonRankSumTest_differential Man page Source code
RTN.analysis Man page Source code
RTN.network.plot Man page Source code
SCT_Harmony_cluster Man page Source code
SNF_Similairity_Hist Man page Source code
Seurat2Monocle3 Man page Source code
build.SVM Man page
build.best.random.forest Man page
build.coxregression.model Man page Source code
build.elastic.net.regression Man page Source code
build.lassoOrRidge.regression Man page Source code
build.logistic.model Man page Source code
build.psm.regression.model Man page
build.randomforest.model Man page Source code
buildEnsembleModel Man page Source code
buildGRangesObj Man page Source code
cal_cnvScore Man page Source code
calculateNMI Man page Source code
cand.cls.box Source code
celline_drug_group_auc_analysis Man page Source code
celline_drug_target_auc_analysis Man page Source code
cellline_drug_gene_correlation Man page Source code
checkHousekeepingCombination Man page Source code
check_diff_gene Man page
clincial_impact Man page Source code
compareROC Man page
compare_GSE.HTSAnalyzer Man page Source code
compare_differential.analysis Man page
compare_differential.ttest.analysis Man page
confidence_interval Man page
confusion_matrix Man page
consensusSubtyping Man page Source code
convert2Scientific Source code
convertDfToNumeric Man page Source code
convertEnsemblDF2SymbolDF Man page Source code
countClassByColumn Man page Source code
count_to_tpm Man page
cross.validation Man page Source code
dataframe2gct_file Man page Source code
decisionCurve.diff.pvalue Man page Source code
decisionCurveAnalysis Man page Source code
decisionCurveAnalysisSimple Man page Source code
determineClusterNumber Man page Source code
dimPlotWithCountBar Man page
download.geo.dataset Man page Source code
draw.expression.dotplot Man page
draw.mutation.type Man page Source code
draw.mutation.type.barplot Man page Source code
draw.target.coverage.plot Man page Source code
drawScatter Man page Source code
draw_confusion_matrix Man page
ensembl_EntrezID Man page Source code
export2CellphoneDB Source code
export2ppt Man page Source code
exportScenicLoom Man page Source code
exportTable Man page Source code
extractSignaturePercent Man page Source code
extractTCGASampleType Man page Source code
feature.selection.4givenMLAlgorithm Man page Source code
feature.selection.RFE Man page Source code
feature.selection.boruta Man page Source code
fillNADataframe Man page Source code
fillSymmetricNATable Man page Source code
filterGenes Man page
findMaxMinColumnNamesForEachRow Man page Source code
findRepeatedGenes Man page Source code
findSomaticSignature Man page Source code
findSurvivalCutPoint Man page Source code
forest_plot Man page
formatTable Man page Source code
fpkm2tpm Man page Source code
gapStat Man page Source code
generate.sequencial.color Man page Source code
generateCombinations Man page Source code
generateGenePairValueDf Man page
generatePairValue Man page
genereateLabelsByGroup Man page Source code
get.AUC Man page
get.TCGA.Project.Clinical Man page Source code
get.TCGA.RNA.FPKM Man page Source code
get.TCGA.miRNAExpression Man page Source code
get.TCGA.sample.project.infomap Man page Source code
get.YoudenIndex Man page
get.all.point.ROC Man page
get.ggsci.color Man page Source code
get.mostDistint.color.palette Man page Source code
get.palette.color Man page Source code
getFastaSummary Man page Source code
getGeneRelatedTranscripts.Gff Man page Source code
getOneRoundCVRes Man page Source code
getProgramName Man page Source code
getPromoterRegions Man page Source code
getTranscriptLength Man page Source code
getTranscriptProteinSequence Man page Source code
get_all_performance_table Man page
get_full_mapping_table Man page Source code
get_individual_candidates_performance Man page
get_performance Man page
group2class_file Man page Source code
groupCorrelation Man page Source code
heatmap.annotation Man page Source code
heatmap.with.lgfold.riskpro Man page Source code
heatmap.with.wordcloud Man page Source code
hello Man page Source code
hyperGeoTest Man page Source code
hyperGeoTest4ContingencyTable Man page Source code
id_mapping Man page Source code
identifySubtypeFromMatrix Man page Source code
iflog2 Man page
is.nan.data.frame Man page Source code
lasso.cox.selection Man page Source code
lasso.cv.select.feature Man page Source code
lasso.select.feature Man page Source code
lasso_best_lamda Man page
limma.differential.cv.selection Man page
limma_differential Man page Source code
load.gmt Man page Source code
load.rsem.matrix Man page Source code
load.salmon.matrix Man page Source code
load10X Man page Source code
loadArrayExpressDataset Man page
loadGff Man page Source code
loadICGC.exp Man page Source code
loadICGC.methy Man page Source code
loadMethylationArraryData Man page Source code
log2dfQuantileNormalization Man page
logit2prob Man page
loo.cv Man page
loo.cv.cox Man page
maf2binaryTable Man page Source code
meltDataFrameByGroup Man page Source code
miRBaseConverter Man page Source code
microarray_limma_differential Man page Source code
multiIntersection Man page Source code
multi_roc_with_ci Man page
multipleHyperGeoTest Man page Source code
multiplePlotPredictedPro Man page
multivariate_cox Man page
multivariate_or Man page
nomogram.plot Man page
norm_find_scale Man page Source code
normalize_miRNACount_toCPM Man page Source code
ntbft Man page Source code
ntbft.boot Man page Source code
oncoPredict Man page Source code
oneway.anova Man page Source code
pairwiseAdonisTest Man page Source code
plot.ntbft Man page Source code
plotClevelandDot Man page Source code
plotJitterBoxplot Man page Source code
plotPCA Man page Source code
plotPie Man page Source code
plotSilhouette Man page Source code
plotUpset Man page Source code
plotVenn Man page Source code
plotVennLegacy Man page Source code
plot_miRCorrelation Man page
plot_waterfall Man page
pre_pseudotime_matrix Man page Source code
prob2logit Man page
pseudoHeatmap Man page Source code
radarSpiderPlot Man page Source code
randomOrderWithinGroup Man page Source code
rangeScale01 Man page Source code
read.cls Source code
read.gct Source code
readICGCExpFile Man page
read_mirdeep2_result Man page Source code
read_mirdeep2_resultDir Man page Source code
reduce_join_list Man page Source code
refSeq_Ensembl Man page Source code
remove.verylong.isoform.gff Man page Source code
removeBatchEffect Man page Source code
return_immune_genes Man page Source code
riskCalibrationPlot Man page Source code
riskCalibrationPlot.default Man page Source code
riskCalibrationPlot.lrm Man page Source code
riskCalibrationPlotMultiple Man page Source code
riskCalibrationPlotSingleComplex Man page Source code
rms_validate Man page Source code
roc_with_ci Man page
runCopyKAT Man page Source code
runCytoTrace1 Man page Source code
runCytoTrace2 Man page Source code
runEPIC Man page Source code
runEstimate Man page Source code
runImmunedeconv Man page Source code
runInferCNV Man page Source code
runMetaFlux Man page Source code
runSlingshot Man page Source code
runWGCNA Man page Source code
run_SNF Man page Source code
run_cellChat Man page Source code
scViolinPlot Man page Source code
scaleDF Man page Source code
scenicHeatmap Man page Source code
show_hcluster Man page Source code
simplifyEnrichment Man page Source code
splitCharacter Man page Source code
splitDataByGroup Man page
splitGroupByCutoff Man page Source code
splitSampleByGroup Man page
ssGSEA Man page Source code
submap Source code
submap.main Source code
submap.perm Source code
subtypeAssociationAnalysis Man page Source code
suppa.event.pie Man page Source code
suppa.get.final.table Man page Source code
surv_ROC_DCA Man page Source code
survivaly_analysis Man page Source code
table2Figure Man page Source code
take.intersection Source code
tanimoto_distance Man page Source code
tcgaShorterBarcode Man page Source code
tcgabiolinks.get.450k.methylation Man page Source code
tcgabiolinks.get.RNA.expression.log2tpm Man page Source code
tcgabiolinks.get.junction.coverage Man page Source code
testCategoricalVariableFreq Man page Source code
thisPath Man page Source code
time_serials_Cindex Man page Source code
ttest_differential Man page Source code
unique_gene_expression Man page Source code
univariate_cox Man page
univariate_cox_sthda Man page
univariate_or Man page
vector.group Man page Source code
volcano_plot Man page Source code
whoAmI Man page Source code
writeGff Man page Source code
ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.

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