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