Man pages for LTLA/diffHic
Differential Analysis of Hi-C Data
| annotatePairs | Annotate bin pairs |
| boxPairs | Put bin pairs into boxes |
| clusterPairs | Cluster bin pairs |
| compartmentalize | Identify genomic compartments |
| connectCounts | Count connecting read pairs |
| consolidatePairs | Consolidate results for interactions |
| correctedContact | Iterative correction of Hi-C counts |
| cutGenome | Cut up the genome |
| diClusters | Cluster significant bin pairs to DIs |
| diffHicUsersGuide | View diffHic user's guide |
| DNaseHiC | Methods for processing DNase Hi-C data |
| domainDirections | Calculate domain directionality |
| enrichedPairs | Collect local enrichment statistics for bin pairs |
| extractPatch | Extract a patch of the interaction space |
| filterDiag | Filtering of diagonal bin pairs |
| filterPeaks | Filter bin pairs for likely peaks |
| filters | Filtering strategies for bin pairs |
| getArea | Get interaction area |
| getPairData | Get read pair data |
| loadData | Load data from an index file |
| marginCounts | Collect marginal counts for each bin |
| mergeCMs | Merge ContactMatrix objects |
| mergePairs | Merge read pairs |
| neighborCounts | Load Hi-C interaction counts |
| normalizeCNV | Normalize CNV biases |
| pairParam | pairParam class and methods |
| plotDI | Construct a plaid plot of differential interactions |
| plotPlaid | Construct a plaid plot of interactions |
| preparePairs | Prepare Hi-C pairs |
| prunePairs | Prune read pairs |
| readMTX2IntSet | Create an InteractionSet from a BED file and Matrix Market... |
| savePairs | Save Hi-C read pairs |
| squareCounts | Load Hi-C interaction counts |
| totalCounts | Get the total counts |
