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Created with Raphaël 2.2.025May18153226Apr181211965428Mar2320139826Feb531Jan302925221918161512111098222Dec2120191815141311429Nov272321201615139727Oct262524191613121120Sep191815148654131Aug302328Jul26242120191830Jun29222120191513982131May2924231918169428Apr2724191024Mar2322151392122Dec9123Nov181420Oct18121116Sep15149626Aug244128Jul8765124Jun151432130May2625201917131211109428Apr2012864124Mar2117161582129Feb26252423854129Jan2726158765418Dec1611982112Nov963228Oct2322211918728Sep2221181716151187331Aug2524201930Jul2923211714133130Jun29242319161511109321May20191230Apr2928272316987131Mar2720181716131211109413Feb123228Jan272114619Dec181712118528Nov272624212014fixed norm count mean per conditionMerge remote-tracking branch 'origin/master'fixed bug concerning biomart database selectionfixed custom mouse igenome buildfixed arg check in dge_bigwigmodernized dge_merge_trepssimplified redundant export in kallisto data aggregationchanged left to inner join when adding gene length for fpkm/tpm normalizationfixed 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 helper