├── .gitignore ├── COSMIC └── cosmic_67_for_HotSpot3D_missense_only.tsv.bz2 ├── Demo ├── Expected │ ├── cmd_list_submit_file │ ├── demo.l0.ad10.r10.mericUns.strInd.subInd.recurrence.clusters │ ├── demo.l0.ad10.r10.mericUns.strInd.subInd.recurrence.clusters.summary │ ├── demo.l0.ad20.pairwise │ ├── demo.weighted.l0.ad10.r10.mericUns.strInd.subInd.recurrence.clusters │ ├── demo.weighted.l0.ad10.r10.mericUns.strInd.subInd.recurrence.clusters.summary │ ├── demo.weighted.l0.ad10.r10.mericUns.strInd.subInd.weight.clusters │ ├── demo.weighted.l0.ad10.r10.mericUns.strInd.subInd.weight.clusters.summary │ └── demo.weighted.l0.ad20.pairwise ├── README_demo ├── demo.maf └── demo.weighted.maf ├── HotSpot3D-1.8.2.tar.gz ├── LICENSE.md ├── README.md ├── bin └── hotspot3d ├── dist.ini ├── lib └── TGI │ ├── Data │ ├── CleanNumber.pm │ └── StringTemplate.pm │ ├── Files │ ├── Clusters.pm │ ├── DrugPairs.pm │ ├── File.pm │ ├── List.pm │ ├── MAF.pm │ ├── Pairwise.pm │ └── PyMOL.pm │ ├── Mutpro │ ├── Distance.pm │ ├── Main │ │ ├── AllMain.pm │ │ ├── BruteForceClustersLines.R │ │ ├── Cluster.pm │ │ ├── ColorScore.R │ │ ├── Density.pm │ │ ├── HorizClustersLines.R │ │ ├── MafSimulator.pm │ │ ├── MembershipProbability.R │ │ ├── Network.pm │ │ ├── Post.pm │ │ ├── Proximity.pm │ │ ├── Significance.pm │ │ ├── Summary.pm │ │ └── Visual.pm │ ├── Pair.pm │ └── Preprocess │ │ ├── AllPreprocess.pm │ │ ├── AminoAcid.pm │ │ ├── Anno.pm │ │ ├── Calpro.pm │ │ ├── Calroi.pm │ │ ├── Complicated.pm │ │ ├── Cosmic.pm │ │ ├── Drugport.pm │ │ ├── Homolog.pm │ │ ├── HugoGene.pm │ │ ├── HugoGeneMethods.pm │ │ ├── PdbStructure.pm │ │ ├── Peptide.pm │ │ ├── Point.pm │ │ ├── Prep.pm │ │ ├── Prior.pm │ │ ├── Statis.pm │ │ ├── Trans.pm │ │ ├── Uniprot.pm │ │ └── Uppro.pm │ ├── ProteinVariant.pm │ └── Variant.pm ├── scripts ├── DensityScripts │ ├── ClusterProbability.pl │ ├── ClustersLines.R │ ├── DensityAll.pl │ ├── DensityVisual.pl │ ├── EasyClustersLines.R │ ├── HorizClustersLines.R │ ├── MembershipProbability.R │ ├── OpticsWithR.pl │ ├── PlotR.R │ ├── README.md │ └── SuperClustersID.pl ├── MafSimulatorScripts │ └── simulate.pl ├── README.annotations ├── addRandomWeight.pl ├── annotate_clusters_HGNC_Kinase.pl ├── annotate_clusters_MAF.pl ├── annotate_clusters_PDB.pl ├── annotate_clusters_domains.pl ├── annotate_clusters_drug_class.pl ├── annotate_clusters_families.pl ├── clusterPDBPresence.drug.pl ├── clusterPDBPresence.pl ├── determine_transcript_lengths.pl ├── filter_PDB.pl ├── genePDBPresence.pl ├── hotspot3d.main.sh └── nStructures.pl └── t └── foo.t /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ding-lab/hotspot3d/HEAD/.gitignore -------------------------------------------------------------------------------- /COSMIC/cosmic_67_for_HotSpot3D_missense_only.tsv.bz2: -------------------------------------------------------------------------------- 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