Software: Hicexplorer
Description
Hicexplorer is a set of tools to process, normalize and visualize Hi-C data.
Available Versions
| Unspecified: | 3.7.2 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/hicexplorer and its home page: https://hicexplorer.readthedocs.io/en/latest/#.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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