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Hicexplorer

Introduction ~~~~~~~~ Hicexplorer is a set of tools to process, normalize and visualize Hi-C data.

For more information, please check its website: https://biocontainers.pro/tools/hicexplorer and its home page: https://hicexplorer.readthedocs.io/en/latest/#.

Versions

  • 3.7.2

Commands ~~~~~~~ - chicAggregateStatistic - chicDifferentialTest - chicExportData - chicPlotViewpoint - chicQualityControl - chicSignificantInteractions - chicViewpoint - chicViewpointBackgroundModel - hicAdjustMatrix - hicAggregateContacts - hicAverageRegions - hicBuildMatrix - hicCompareMatrices - hicCompartmentalization - hicConvertFormat - hicCorrectMatrix - hicCorrelate - hicCreateThresholdFile - hicDetectLoops - hicDifferentialTAD - hicexplorer - hicFindEnrichedContacts - hicFindRestSite - hicFindTADs - hicHyperoptDetectLoops - hicHyperoptDetectLoopsHiCCUPS - hicInfo - hicInterIntraTAD - hicMergeDomains - hicMergeLoops - hicMergeMatrixBins - hicMergeTADbins - hicNormalize - hicPCA - hicPlotAverageRegions - hicPlotDistVsCounts - hicPlotMatrix - hicPlotSVL - hicPlotTADs - hicPlotViewpoint - hicQC - hicQuickQC - hicSumMatrices - hicTADClassifier - hicTrainTADClassifier - hicTransform - hicValidateLocations

Module

You can load the modules by:

module load biocontainers
module load hicexplorer

Example job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Hicexplorer on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hicexplorer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers hicexplorer