# Configs

## InputConfigs

### Peaks

### rnaSeq

### geneIDs

### geneAnnotationFile

### sameStages

### genome

### biomartSpecies

### seqType

## MixOptions

### blackListPath

### differentialPeakSignals

### maxSpaceBetweenPeaks

### minOccurrence

### mixMutuallyExclusive

### perform

### tfBindingSiteSearch

### seqType

## DeSeq2

### tpmFilter

### batches

### countFilter

## TEPIC

### PWMs

### transcriptBased

### columnBedfile

### windowSize

### loopListFile

### loopWindows

### exponentialDecay

### doNotNormalizePeakLength

### maxMinutesPerChromosome

### doZip

### originalDecay

### psemsLengthFile

### pValue

### chromosomePrefix

### onlyPeakFeatures

### entireGeneBody

### twoBitFile

### onlyDNasePeaks

### inputReferenceGenome

### bedChromatinSignal

### affinityCutoff

## DYNAMITE

### outVar

### iFolds

### oFolds

### performance

### alpha

### randomize

## Plots

### topKTargetGenes

### thre
