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Created with Raphaël 2.2.024Jul2120191830Jun29222120191513982131May2924231918169428Apr2724191024Mar2322151392122Dec9123Nov181420Oct18121116Sep15149626Aug244128Jul8765124Jun151432130May2625201917131211109428Apr2012864124Mar2117161582129Feb26252423854129Jan2726158765418Dec1611982112Nov963228Oct2322211918728Sep2221181716151187331Aug2524201930Jul2923211714133130Jun29242319161511109321May20191230Apr2928272316987131Mar2720181716131211109413Feb123228Jan272114619Dec181712118528Nov272624212014fixed count filteradjusted path to ngs_tools on clusterMerge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_toolsadded outliers analysisupdated PCA with and without batch effect and updated to datautils/v1.42/R/ggplot_commons.Rstarted compilation of dup-radar reference data setsMerge remote-tracking branch 'origin/master'added dge_analyze_duplicates.shadded model dup-radar model parameter correlation plotfinished basic integration of dupradarcont duplicate analysisadded picard setuprun bc outside of STAR wrapperstarted duplicate analysisfixed typouse {} for variables where possiblemore robust environment check in dge templatemade deeptools path user independentfixed bioinfo paths in star templateadded r path; use PRJ_NAME everywhereadedd umask settings for dge templateadded check for samtoolsuse user dependent ngs-tools pathremoved user dependency from star templatechanged pca to color in all effecdtsadded cor matrix output to dge_bam_correlateupdated kallisto setupcosmetics; updated kotlin dependenciesrestored correct grouping in fpkm exportadded top20 matrix visualizationimproved tpm export. disabled ihw. more args checkingfixes #14continued docker base imageadded kscript to docker base imagestarted bioinfo base docker imageadded hsap ncbi build to igenome cacheadded bowtie index for custom hsap buildround tpms for exportkeep gene ids in enrichment reportadded more comments