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Created with Raphaël 2.2.018Apr1211965428Mar2320139826Feb531Jan302925221918161512111098222Dec2120191815141311429Nov272321201615139727Oct262524191613121120Sep191815148654131Aug302328Jul26242120191830Jun29222120191513982131May2924231918169428Apr2724191024Mar2322151392122Dec9123Nov181420Oct18121116Sep15149626Aug244128Jul8765124Jun151432130May2625201917131211109428Apr2012864124Mar2117161582129Feb26252423854129Jan2726158765418Dec1611982112Nov963228Oct2322211918728Sep2221181716151187331Aug2524201930Jul2923211714133130Jun29242319161511109321May20191230Apr2928272316987131Mar2720181716131211109413Feb123228Jan272114619Dec181712118528Nov272624212014fixed output prefixing in limma workflowadded shebang line to limma workflowfixed mouse igenome buildreduced bootstrapping for kallistonew mouse ens92 ensembl buildnew mouse igenomes buildexcluded patch level from r-release checkremoved unused exportlimma: Added pca plot for normalized datarevision set intersection helpersv10v10added score correlation plot to limma workflowadded `as_int_matrix` and `expr_matrix_to_df` to diffex commonsprint contrastsmerged with remoteadded support for design; fixed q/p cutoff parameterschanged input to counts matrix and design; changed handeling of input data; added sequencing saturation plotadded information on UMI-tools docker containeradded option to directly provide biomart databaseadded installation of lastadded support for custom designs to limma workflowrevised imputation scheme for ms dataupdated limma instructionsmoved limma workflow into ngs toolsremoved unused fileschange "fetch the data" section to prevent disclosure of login detailsadded install instructions for flashadded more adapters from Iancont cutadapt pe report (still incomplete)allow to override custom star params with environment variableadded standard illumina adapters as reference for cutadaptimpl cutadapt report for pe dataupdated igv and added helperstarted cutadapt summary report migration to latest versionimpl bonobo genome buildadded more debugging vis for batch correction utilcreate session file after pathway vismatched node.sum config with cp_enrichment.Rv9v9removed duplicated pathway renderingused fixed port for expression exploreradded icon to expression explorer