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Created with Raphaël 2.2.030Jun29222120191513982131May2924231918169428Apr2724191024Mar2322151392122Dec9123Nov181420Oct18121116Sep15149626Aug244128Jul8765124Jun151432130May2625201917131211109428Apr2012864124Mar2117161582129Feb26252423854129Jan2726158765418Dec1611982112Nov963228Oct2322211918728Sep2221181716151187331Aug2524201930Jul2923211714133130Jun29242319161511109321May20191230Apr2928272316987131Mar2720181716131211109413Feb123228Jan272114619Dec181712118528Nov272624212014fixed 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 commentsfinished basic tx architecture enrichment reportadded helper script to convert counts to tpm and fpkmcont dexseq retention analysisstarted gene feature enrichment analysiscont custom hsap igenome buildincreased memory to build star indexadded custom hsap build; source core_utils in dge_utilsfixed stranding in analysisfixed: star tmp files are not removedfinished basic impl of dexseq protocolalso export directed hits table for enrichment analysisimproved enrichement reportMerge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_toolsadded more sections to template