├── .Rbuildignore ├── .dockerignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── docker.yml ├── .gitignore ├── DESCRIPTION ├── Dockerfile ├── NAMESPACE ├── R ├── BFF_Demux.R ├── CellHashing.R ├── DemuxEM.R ├── DropletUtils_Demux.R ├── GMM_Demux.R ├── Multiseq.R ├── Normalization.R ├── Preprocessing.R ├── SeqND_Demux.R ├── Seurat_HTO_Demux.R ├── Threshold_Demux.R ├── Utils.R ├── Visualization.R └── demuxmix.R ├── README.md ├── _pkgdown.yml ├── cellhashR.iml ├── inst └── rmd │ └── cellhashR.rmd ├── man ├── AppendCellHashing.Rd ├── CalculateSaturationFor10x.Rd ├── CallAndGenerateReport.Rd ├── EstimateMultipletRate.Rd ├── GenerateCellHashingCalls.Rd ├── GetExampleMarkdown.Rd ├── GetSeed.Rd ├── ParameterScan.Rd ├── PlotLibrarySaturation.Rd ├── PlotLibrarySaturationByMarker.Rd ├── PlotNormalizationQC.Rd ├── ProcessCountMatrix.Rd ├── SetSeed.Rd └── SummarizeCellsByClassification.Rd ├── tests ├── testdata │ ├── 438-21-GEX │ │ ├── 438-21-GEX.unknown.txt │ │ ├── 438-21-raw_feature_bc_matrix.h5 │ │ ├── read_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ ├── run_report.yaml │ │ ├── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── validHashingBarcodes.csv │ ├── 438-24-GEX │ │ ├── 438-24-GEX.unknown.txt │ │ ├── run_report.yaml │ │ ├── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── validHashingBarcodes.csv │ ├── 449-1-GEX │ │ ├── 449-1-GEX.unknown.txt │ │ ├── run_report.yaml │ │ ├── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── validHashingBarcodes.csv │ ├── 457-1-GEX │ │ ├── 457-1-GEX.unknown.txt │ │ ├── run_report.yaml │ │ ├── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── validHashingBarcodes.csv │ ├── 458-6-GEX.citeSeqCounts.2.citeseq │ │ ├── read_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ ├── 471-1-GEX │ │ ├── 471-1-GEX.unknown.txt │ │ ├── run_report.yaml │ │ ├── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── validHashingBarcodes.csv │ ├── 471-2-GEX │ │ ├── 471-2-GEX.unknown.txt │ │ ├── run_report.yaml │ │ ├── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── validHashingBarcodes.csv │ ├── 483-3-GEX │ │ ├── 483-3-GEX.unknown.txt │ │ ├── run_report.yaml │ │ ├── umi_count │ │ │ ├── barcodes.tsv.gz │ │ │ ├── features.tsv.gz │ │ │ └── matrix.mtx.gz │ │ └── validHashingBarcodes.csv │ ├── 563-3-TCR.hashing.rawCounts.rds │ ├── 568-1-TCR.hashing.rawCounts.rds │ ├── MS │ │ └── cell_type_counts.csv │ ├── allMsBarcodes.txt │ └── cellHashing │ │ ├── 247-1-hashTagCounts.txt │ │ ├── 249-2-HTO_cellHashingRawCounts.txt │ │ ├── 282-1-HTO_cellHashingRawCounts.txt │ │ ├── 282-1-whitelist.txt │ │ ├── 283-cellbarcodeToHTO.calls.citeSeqCounts.txt │ │ ├── 283-validCellIndexes.csv │ │ └── umi_count │ │ ├── barcodes.tsv.gz │ │ ├── features.tsv.gz │ │ └── matrix.mtx.gz ├── testthat.R └── testthat │ ├── test-appendhashing.R │ ├── test-bff.R │ ├── test-cellhashing.R │ ├── test-demuxem.R │ ├── test-demuxmix.R │ ├── test-gmmdemux.R │ └── testing-data.R └── vignettes ├── .gitignore ├── BFF-example_files ├── .DS_Store └── figure-html │ ├── NormalizationQC-1.png │ ├── NormalizationQC-12.png │ ├── NormalizationQC-13.png │ ├── NormalizationQC-16.png │ ├── NormalizationQC-2.png │ ├── NormalizationQC-3.png │ ├── NormalizationQC-4.png │ ├── NormalizationQC-5.png │ ├── NormalizationQC-8.png │ ├── NormalizationQC-9.png │ ├── QC_fig.png │ ├── sim_curves.png │ ├── unnamed-chunk-2-18.png │ ├── unnamed-chunk-2-19.png │ ├── unnamed-chunk-2-35.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-3-19.png │ ├── unnamed-chunk-3-35.png │ ├── unnamed-chunk-4-19.png │ ├── unnamed-chunk-4-35.png │ ├── unnamed-chunk-5-19.png │ └── unnamed-chunk-5-35.png ├── Benchmark-example_files ├── .DS_Store └── figure-html │ ├── Benchmark_fig.png │ ├── FinalCalls-1.png │ ├── GenerateCalls-1.png │ ├── GenerateCalls-17.png │ ├── GenerateCalls-19.png │ ├── GenerateCalls-2.png │ ├── GenerateCalls-20.png │ ├── GenerateCalls-3.png │ ├── GenerateCalls-33.png │ ├── GenerateCalls-35.png │ ├── GenerateCalls-4.png │ ├── GenerateCalls-48.png │ ├── GenerateCalls-49.png │ ├── GenerateCalls-50.png │ ├── GenerateCalls-51.png │ ├── GenerateCalls-64.png │ ├── GenerateCalls-65.png │ ├── GenerateCalls-66.png │ ├── GenerateCalls-79.png │ ├── GenerateCalls-80.png │ ├── GenerateCalls-81.png │ ├── GenerateCalls-82.png │ └── GenerateCalls-95.png ├── QC-example_files └── figure-html │ ├── NormalizationQC-1.png │ ├── NormalizationQC-10.png │ ├── NormalizationQC-11.png │ ├── NormalizationQC-12.png │ ├── NormalizationQC-13.png │ ├── NormalizationQC-14.png │ ├── NormalizationQC-15.png │ ├── NormalizationQC-16.png │ ├── 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