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Created with Raphaël 2.2.022May121Apr2010Feb324Nov27Oct2526May1999Dec19Nov25Oct22151217Sep10313Aug629Jul1312Upload virus_in_paper.zipmastermasterRemove old SPSP dumpAdd viruses used in paperRemoved global paths.Update analysis of 0-snp time windowsRemove draft paper notebookClean paper notebookUpdated normalized correlation plot, computed boxplots for superspreder events, updated correlation cluster size vs num cantons plotInvestigate filtered sequences omicronAdd cluster density normalized by the number of sequences in the cluster analysisExecute latest resultsUpdate LicenseBeautify readme.mdAdd readme picsUse get_snp_cluster package & documentRepository restructureUpdate README.mdUpdate README.mdClean SPSP-paper-plots.ipynbAdd paper plots notebookmake cluster tool callableMerge branch 'master' of https://gitlab.sib.swiss/SPSP/sarscov2/cluster-detectionReplace hierarchical clustering by UnionFind to merge 1-SNP clustersUpload New FileDelete SPSP-dump_220421.tsv.zipBash scriptMerge branch 'master' of https://gitlab.sib.swiss/SPSP/sarscov2/cluster-detectionCode update for new spsp data formatDump1-non-sensitiveAdd new directoryUpdate README.md to add licenseUpdate snakemake-minimal version.Document and clean code.Remove HC_THRESHOLD input parameter.Fix output in clusters summarySmall updates to cluster merge.Fix libraries and dependency bugsUse hierarchical clustering as method to merge 1-SNP clustersRemove personal directories.Update README