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  • belicova_mouse__20170519
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Created with Raphaël 2.2.09Jan8222Dec2120191815141311429Nov272321201615139727Oct262524191613121120Sep191815148654131Aug302328Jul26242120191830Jun29222120191513982131May2924231918169428Apr2724191024Mar2322151392122Dec9123Nov181420Oct18121116Sep15149626Aug244128Jul8765124Jun151432130May2625201917131211109428Apr2012864124Mar2117161582129Feb26252423854129Jan2726158765418Dec1611982112Nov963228Oct2322211918728Sep2221181716151187331Aug2524201930Jul2923211714133130Jun29242319161511109321May20191230Apr2928272316987131Mar2720181716131211109413Feb123228Jan272114619Dec181712118528Nov272624212014fixed bug in the step where the list of SingleCellExperiment objects is createdbetter indexing parallelizationseparated genome indexing into own scriptMerge remote-tracking branch 'origin/master'started script to perform quality control of single cell RNAseq data. This is the first script of our new workflow, i.e. sc_workflow/Merge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_toolsadded appifyadded platform independent symlinksstarted script to compare kallisto and star dataadded input argument '<cdna_file_name>', genome information, sample information and plot of the proportion of pseudoaligned readsrun_kallisto(): saved kallisto log files and passed information on the used cdna file to collect_kallisto_data.Radded output of pseudoalignments as sam and bam filesremoved _linuxrefined batch correction toolingmoved call of the collect_kallisto_data.R script to run_kallisto() in the dge_utils.sh scriptincluded function to build_kallisto_index() and included the call of collect_kallisto_data.R in the run_kallisto functionremoved the prerequisite to give basic_design.txt as inputincluded tpms_by_gene in kallisto_results.txt outputincluded command to create 'expression explorer' appincluded function to create 'expression explorer' app (i.e. dge_create_explorer_app)created script to analyse kallisto dataadded mapping with kallisto and kallisto data analysisadded path to kallistoMerge remote-tracking branch 'origin/master'created bash script to run the expression explorer app either via bash or as a 'proper' app when processed with appifyMerge remote-tracking branch 'origin/master'changed to use heatmaplyfixed batch correction to include treatmentsuse rlog instead of vstMerge remote-tracking branch 'origin/master'added run_kallisto functioncosmeticsdo second round of pca and clustering after correctiondoc cleanupimpl correlation analysis and batch removalMerge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_toolsMerge remote-tracking branch 'origin/master'print basic_design (i.e. replicates2samples) to filechanged layout; removed gene information text; included options (confidence interval, line); enabled sorting of samples; allowed to plot more than one gene at onceexport qc summary table in fastqc report