├── .gitignore ├── CHANGELOG.rst ├── CMake ├── FindBamTools.cmake ├── FindR.cmake └── deps.cmake ├── CMakeLists.txt ├── Estimation ├── BamProcessing │ ├── BamController.cpp │ ├── BamController.h │ ├── BamProcessor.cpp │ ├── BamProcessor.h │ ├── BamProcessorAbstract.cpp │ ├── BamProcessorAbstract.h │ ├── BamTags.cpp │ ├── BamTags.h │ ├── FilledBamParamsParser.cpp │ ├── FilledBamParamsParser.h │ ├── FilteringBamProcessor.cpp │ ├── FilteringBamProcessor.h │ ├── ReadMapParamsParser.cpp │ ├── ReadMapParamsParser.h │ ├── ReadParamsParser.cpp │ └── ReadParamsParser.h ├── Cell.cpp ├── Cell.h ├── CellsDataContainer.cpp ├── CellsDataContainer.h ├── Gene.cpp ├── Gene.h ├── Merge │ ├── BarcodesParsing │ │ ├── BarcodesParser.cpp │ │ ├── BarcodesParser.h │ │ ├── ConstLengthBarcodesParser.cpp │ │ ├── ConstLengthBarcodesParser.h │ │ ├── InDropBarcodesParser.cpp │ │ └── InDropBarcodesParser.h │ ├── BrokenRealBarcodesMergeStrategy.cpp │ ├── BrokenRealBarcodesMergeStrategy.h │ ├── DummyMergeStrategy.h │ ├── MergeAllMergeStrategy.h │ ├── MergeProbabilityValidator.cpp │ ├── MergeProbabilityValidator.h │ ├── MergeStrategyAbstract.cpp │ ├── MergeStrategyAbstract.h │ ├── MergeStrategyBase.cpp │ ├── MergeStrategyBase.h │ ├── MergeStrategyFactory.cpp │ ├── MergeStrategyFactory.h │ ├── PoissonRealBarcodesMergeStrategy.cpp │ ├── PoissonRealBarcodesMergeStrategy.h │ ├── PoissonSimpleMergeStrategy.cpp │ ├── PoissonSimpleMergeStrategy.h │ ├── PoissonTargetEstimator.cpp │ ├── PoissonTargetEstimator.h │ ├── RealBarcodesMergeStrategy.cpp │ ├── RealBarcodesMergeStrategy.h │ ├── SimpleMergeStrategy.cpp │ ├── SimpleMergeStrategy.h │ └── UMIs │ │ ├── MergeUMIsStrategyAbstract.cpp │ │ ├── MergeUMIsStrategyAbstract.h │ │ ├── MergeUMIsStrategyDirectional.cpp │ │ ├── MergeUMIsStrategyDirectional.h │ │ ├── MergeUMIsStrategySimple.cpp │ │ └── MergeUMIsStrategySimple.h ├── ReadInfo.h ├── ReadParametersEfficient.cpp ├── ReadParametersEfficient.h ├── ResultsPrinter.cpp ├── ResultsPrinter.h ├── Stats.cpp ├── Stats.h ├── StringIndexer.cpp ├── StringIndexer.h ├── UMI.cpp └── UMI.h ├── LICENSE.md ├── README.rst ├── TagsSearch ├── ConcurrentGzWriter.cpp ├── ConcurrentGzWriter.h ├── Counters │ ├── MultiSpacerOutcomesCounter.cpp │ ├── MultiSpacerOutcomesCounter.h │ ├── OutcomesCounter.cpp │ ├── OutcomesCounter.h │ ├── TrimsCounter.cpp │ ├── TrimsCounter.h │ ├── TwoBarcodesCounter.cpp │ └── TwoBarcodesCounter.h ├── FastQReader.cpp ├── FastQReader.h ├── FixPosSpacerTagsFinder.cpp ├── FixPosSpacerTagsFinder.h ├── IClipTagsFinder.cpp ├── IClipTagsFinder.h ├── IndropV1TagsFinder.cpp ├── IndropV1TagsFinder.h ├── IndropV3LibsTagsFinder.cpp ├── IndropV3LibsTagsFinder.h ├── IndropV3TagsFinder.cpp ├── IndropV3TagsFinder.h ├── SpacerFinder.cpp ├── SpacerFinder.h ├── SplitSeqTagsFinder.cpp ├── SplitSeqTagsFinder.h ├── TagsFinderBase.cpp └── TagsFinderBase.h ├── Tests ├── TestEstimation.cpp ├── TestEstimationMergeProbs.cpp ├── TestTagsSearch.cpp └── TestTools.cpp ├── Tools ├── BlockingConcurrentQueue.h ├── CollisionsAdjuster.cpp ├── CollisionsAdjuster.h ├── GeneAnnotation │ ├── GtfRecord.cpp │ ├── GtfRecord.h │ ├── Interval.cpp │ ├── Interval.h │ ├── IntervalsContainer.h │ ├── RefGenesContainer.cpp │ └── RefGenesContainer.h ├── IndexedValue.h ├── Logs.cpp ├── Logs.h ├── ReadParameters.cpp ├── ReadParameters.h ├── ScSpConcurrentQueue.h ├── UtilFunctions.cpp ├── UtilFunctions.h ├── atomicops.h └── readerwriterqueue.h ├── configs ├── 10x.xml ├── cel_seq2.xml ├── config_desc.xml ├── drop_seq.xml ├── drop_seq_velocyto.xml ├── iclip.xml ├── indrop_v1_2.xml ├── indrop_v3.xml ├── seq_well.xml └── split_seq.xml ├── data ├── SRR1784310_curve.rds ├── barcodes │ ├── 10x_aug_2016_split │ ├── 10x_v2_0_split │ ├── indrop_v1_2 │ ├── indrop_v3 │ ├── split_seq │ └── test_est ├── genesets_human.rds ├── genesets_mouse.rds ├── gtf │ ├── gtf_test.gtf.gz │ ├── hg19_genes.gtf.gz │ ├── hg19_genes_10x.gtf.gz │ ├── mm10_genes.gtf.gz │ ├── refflat_ucsc_mm10.gtf.gz │ ├── refflat_ucsc_mm10.trimmed.bed.gz │ └── refflat_ucsc_mm10_exons.gtf.gz └── mit_genes_human.rds ├── dockers ├── centos6 │ └── Dockerfile ├── centos7 │ └── Dockerfile └── debian9 │ └── Dockerfile ├── docs ├── .readthedocs.yml ├── Makefile ├── alignment.rst ├── conf.py ├── configuration.rst ├── development.rst ├── dropest.rst ├── dropestr.rst ├── dropreport.rst ├── droptag.rst ├── index.rst ├── requirements.txt └── setup.rst ├── dropReport.Rsc ├── dropest.cpp ├── dropestr ├── .Rbuildignore ├── .gitignore ├── CMakeLists.txt ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── RcppExports.R │ ├── cell_number.R │ ├── data.R │ ├── kde_classifier.R │ ├── low_quality_cells.R │ ├── quality_control.R │ ├── umi_classifier.R │ ├── umi_correction.R │ └── utils.R ├── data │ ├── lq_cells_data.rda │ ├── reads_per_umi_per_cell.rda │ └── saturation_srr1784312.rda ├── dropestr.Rproj ├── inst │ └── include │ │ ├── ClassifierData.h │ │ ├── dropestr.h │ │ └── umi_processing.h ├── man │ ├── ArrayDerivative.Rd │ ├── Center.Rd │ ├── EstimateCellsNumber.Rd │ ├── EstimateSaturation.Rd │ ├── FillAdjacentUmisData.Rd │ ├── FractionSmoothScatter.Rd │ ├── GetLongestTrue.Rd │ ├── GetOptimalPcs.Rd │ ├── GetUmisDistribution.Rd │ ├── Normalize.Rd │ ├── PlotCellScores.Rd │ ├── PlotCellsNumberHist.Rd │ ├── PlotCellsNumberLine.Rd │ ├── PlotCellsNumberSummary.Rd │ ├── PlotGenesPerCell.Rd │ ├── PlotIntergenicFractionByChromosomes.Rd │ ├── PlotReadsPerUmiByCells.Rd │ ├── PlotSaturationEstimates.Rd │ ├── PlotUmisDistribution.Rd │ ├── PredictKDE.Rd │ ├── PrepareCellsNumberPlot.Rd │ ├── PrepareLqCellsData.Rd │ ├── Scale.Rd │ ├── ScoreCells.Rd │ ├── ScorePipelineCells.Rd │ ├── TrainKDE.Rd │ ├── hello.Rd │ ├── reads_per_umi_per_cell.Rd │ └── saturation_srr1784312.Rd ├── missfont.log ├── src │ ├── .gitignore │ ├── ClassifierData.cpp │ ├── Makevars │ ├── RcppExports.cpp │ ├── adjacent_umis_estimation.cpp │ ├── classification.cpp │ ├── collisions_adjustment.cpp │ ├── rcpp_wrappers.cpp │ └── utils.cpp └── vignettes │ ├── low-quality-cells.Rmd │ └── umi-correction.Rmd 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