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| FisHiCal-package | Iterative FISH-based Calibration of Hi-C Data |
| calibHiC | in-silico 100*100 calibrated Hi-C contact matrix |
| calibrate | Hi-C calibration |
| conf | A 3D random configuration of 100 points |
| findMatchingIndices | Find matching Hi-C bins for FISH probes, using mid-points |
| FisHiCal | Iterative FISH-based Calibration of Hi-C Data |
| getInfoLevelForChr | Compute the information level for a given chromosome after calibration |
| hic | in-silico 100*100 Hi-C contact matrix with with 5% noise |
| lsmacof | 3D reconstruction from Hi-C distances |
| match | in-silico FISH distances and matching Hi-C frequencies with 5% noise |
| plotInc | Plot a spatial inconsistency |
| prepareCalib | Prepare Hi-C calibration |
| prepareData | Match FISH distances and Hi-C frequencies for calibration |
| searchInc | Search for spatial inconsistencies |
| spatialInc | Spatial inconsistencies detected for loci in fibroblasts chromosome 1 |
| summaryInc | Summarize spatial inconsistencies. |
| updateCalib | Update a parameter value in the calibration model |