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