Predicting the target genes for regulatory elements

annotateGenomicRegions | Hierarchically annotates input GRanges object with... |

annotateRegionToTrait | Add associated traits to the interaction object |

associateReg2Gene | Associate regulatory regions to genes |

assocTable2 | this function creates a table of keys and pvals from a... |

benchmarkAssociations | Benchmarks reg2gene models using benchmark data |

benchmarkAssociationssimple | Benchmarks help function |

benchPlotHelp | Plots enhancer-promoter interactions |

bwToGeneExp | Quantifies gene expression measured by RNA-Seq |

compareModelStat | Reports a number of statistically significant enhancer~... |

compareReg2Traits | Compare two objects of genomic region~gene~trait associations |

confusionMatrix | ConfusionTable statistics for the benchmarked reg2Gene object |

corMat | Correlation between a col matrix and a vector |

corResample | Correlation with resampling p-values |

dcorMat | Distance correlation between a col matrix and a vector |

dcorResample | Distance correlation with resampling based p-values |

detectGeneEnhPresence | GRanges contains gene+enhancer info |

estimateGammaPval | Estimate P-values from resampling statistics using Gamma... |

exonExpressionStrandAdjusted | Function that quantifies exon expression based on strand... |

extractInfo | Help f() to extract info about cohort/method/algorithm |

filterPreBenchGIsimple | Filtering help function |

forceByname | Benchmarks help function - forceByName |

getGeneEnhScoresDF | extract gene-enhancer scores from GRanges object |

glmnetResample | internal function that uses glmnet for prediction |

grlist2GI | convert GRangesList to GInteractions |

grlist2gr | convert GRangesList to GRanges with associated regulatory... |

GRReg1_toy | GRanges example to test various functions from reg2gene |

GRReg2_toy | Sample file for benchmark dataset |

grReorg | Help for grlist2gr() |

makeIndexTable | Creates Index table of files produced by reg2gene data... |

manyZeros | decide if the input colum from a matrix has many zeros |

metaAssociations | meta-analysis for regulatory region and gene associations |

ModellingTest | GRanges example to test modelling of associateReg2gene... |

normalizeScores | Function that runs normalization for the quantified... |

perGeneModelling | Function returns output of called modelling procedure... |

plotGEEA | Scatterplots of enhancer activity~gene expression for max 16... |

plotGenomeInteractions | Plots enhancer-promoter interactions |

quantifyGeneExpression | Function that quantifies gene expression based on... |

qvaluCal | internal qvalue calculation function |

reg2gene | reg2gene: An R package for predicting the target genes for... |

regActivity | Calculates regulatory activity over pre-defined regions |

regActivityAroundTSS | Identify regulatory regions around provided TSSes |

rfResample | internal RandomForest prediction function |

scoresAsMcols | Function that rearranges list of scores calculated per cell... |

selectEP | Returns N TOP/BOTTOM/RANDOM associations per... |

stepwise.complete.cases | Stepwise complete cases method |

voteAssociations | Majority vote decision for (regulatory region)-gene... |

votedEP | Returns voted EP pairs for the combination of cohort/method/... |

zeroVar | decide if the input colum matrix has zero variation |

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