| sevenC-package | Computational chromosome conformation capture by correlation of ChIP-seq at CTCF motifs (7C) | 
| addCor | Add correlation of ChIP-seq coverage to motif pairs. | 
| addCovCor | Add correlation of anchor signals to pairs of close genomic regions. | 
| addCovToGR | Add coverage to regions in 'GRanges' object. | 
| addInteractionSupport | Add column to 'GInteractions' with overlap support. | 
| addMotifScore | Add motif score of anchors. | 
| addStrandCombination | Add combination of anchor strand orientation. | 
| cutoffBest10 | Default optimal cutoff value of logistic regression. | 
| cutoffByTF | Optimal cutoff values for logistic regression models. | 
| getCisPairs | Build a 'GInteractions' object with all pairs of input 'GRanges' within a given distance. | 
| getOutOfBound | Get out of chromosomal bound ranges. | 
| modelBest10Avg | Default parameters for logistic regression model in sevenC. | 
| motif.hg19.CTCF | CTCF motif locations in human genome hg19. | 
| motif.hg19.CTCF.chr22 | CTCF motif locations on chromosome 22 in human genome hg19. | 
| motif.hg19.CTCF.chr22.cov | CTCF motifs on human chromosome 22 with example coverage. | 
| noZeroVar | returns indices of columns with non-zero variance | 
| parseLoopsRao | Parse chromatin loops from Rao et al. 2014 as strict 'GInteractions'. | 
| parseLoopsTang | Parse chromatin interactions from Tang et al. 2015 as 'GInteractions'. | 
| predLogit | Predict interaction probability using logistic regression model. | 
| predLoops | Predict looping interactions. | 
| prepareCisPairs | Prepares motif pairs as 'GInteractions' and add genomic features. | 
| sevenC | Computational chromosome conformation capture by correlation of ChIP-seq at CTCF motifs (7C) | 
| slideMean | Sliding mean over x of intervals of size k | 
| TFspecificModels | TF specific parameters for logistic regression in sevenC |