Package: gcMapExplorer
Genome Contact Map Explorer - gcMapExplorerIt is a platform to visualize and analyze the contact maps that are generated from Hi-C experiments. This package is developed by considering the huge size of contact maps at very fine resolution. It containsGraphical user interface - Several windows like applications to perform tasks (See below tables).Command Line Interface - Several commands to perform tasks (See below tables).Application Programming Interface- It can be used to perform analysis by any mathematical operations through programming.For more details, visit:gcMapExplorer HomepageFor Discussion and Questions, visitthis forumFeaturesSupport forhuge contact maps- Use of Disk instead of RAM - Matrices/arrays are stored in Disks -
mathematical operations by directly reading/writing from/to Disks,without loading them into RAMAbrowserwith rich interfaces
forComparativeandInteractivevisualization oftwo dimensional contact mapsalong
withgenomic datasetssuch as produced by DNase-seq, ChIP-seq, RNA-seq etc.Contact maps can bezoomed in/outfrom finest resolution to whole chromosome level.Rich customizations ofcolor scale for contact mapsvisualizationRich customizations ofX- and Y- axis properties.Save visualization states and view-pointsfor later browsingNormalization of contact mapsbyIterative Correction(IC)Knight-Ruiz Matrix Balancing(KR)Vanilla-Coverage(VC)Distance-FrequencyAnew file formatbased on HDF5 forgenome contact mapandgenomic track datasets.Portable,platform independentand can be read through C/C++, JAVA, Python and R programming language.Very fast to read- fast browsing of contact maps and genomic datasetsAnother file format forchromosomal contact map- much faster than above format to read/write but not compact. Suitable for performing calculations.A GUI interface and commandsto convert Coordinate Sparse, Pair Coordinate Sparse, HOMER Interaction matrix, Bin-Contact formats into the new gcmap and ccmap formats.Commandto convert juicebox/juicer hic format to gcmap.Interface and commands toconvert bigWig/wig/bed file to genomic track dataset h5 file.Interface and commands forNormalization of contact maps.Publication ready images at one click.CitationRajendra Kumar, Haitham Sobhy, Per Stenberg and Ludvig Lizana.Genome Contact Map Explorer - A platform for the comparison, interactive visualization and analysis of genome contact maps.Nucleic Acids Res.(2017).Interfaces and CommandsUsageRungcMapExplorercommand on terminal to get list of all sub-commands.Following sub-commands are available:Graphical User Interface ApplicationsCommandFunctionbrowserInteractive Browser for genomic contact mapscmapImporterInterface to import contact maps and datasetscmapNormalizerInterface to normalize contact mapsh5ConverterInterface to convert bigWig/wig/bed file to h5 fileCommands to import Hi-C dataCommandFunctioncoo2cmapImport COO sparse matrix format to ccmap or gcmappairCoo2cmapImport map from files similar to paired COO formathomer2cmapImport HOMER Hi-C interaction matrix to ccmap or gcmapbc2cmapImport Bin-Contact format files to ccmap or gcmaphic2gcmapImport hic to gcmapCommands to convert bigWig/wig/bed to h5CommandFunctionbigwig2h5Convert a bigWig file to HDF5 format h5 filewig2h5Convert a wig file to HDF5 format h5 filebed2h5Convert a bed file to HDF5 format h5 fileencode2h5Download and convert ENCODE datasets to HDF5 format h5 filesCommands to normalize Hi-C mapCommandFunctionnormKRNormalization using Knight-Ruiz matrix balancingnormVCNormalization using Vanilla-Coverage methodnormICNormalization using Iterative CorrectionnormMCFSScale maps using Median/Mean Contact FrequencyCommands for AnalysisCommandFunctioncorrBWcmapsCalculate correlation between contact mapsConfiguration utilityCommandFunctionconfigTo print configuration file and clean scratch directoryCommand helpRungcMapExplorer<sub-commands>-hcommand.For example:gcMapExplorer normKR-hgcMapExplorer coo2cmap-h