Files in BimberLab/cellhashR
A Package for Demultiplexing Cell Hashing Data
.Rbuildignore
.dockerignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yml
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
R/BFF_Demux.R
R/CellHashing.R
R/DemuxEM.R
R/DropletUtils_Demux.R
R/GMM_Demux.R
R/Multiseq.R
R/Normalization.R
R/Preprocessing.R
R/SeqND_Demux.R
R/Seurat_HTO_Demux.R
R/Threshold_Demux.R
R/Utils.R
R/Visualization.R
R/demuxmix.R
README.md
_pkgdown.yml
cellhashR.iml
inst/rmd/cellhashR.rmd
man/AppendCellHashing.Rd
man/CalculateSaturationFor10x.Rd
man/CallAndGenerateReport.Rd
man/EstimateMultipletRate.Rd
man/GenerateCellHashingCalls.Rd
man/GetExampleMarkdown.Rd
man/GetSeed.Rd
man/ParameterScan.Rd
man/PlotLibrarySaturation.Rd
man/PlotLibrarySaturationByMarker.Rd
man/PlotNormalizationQC.Rd
man/ProcessCountMatrix.Rd
man/SetSeed.Rd
man/SummarizeCellsByClassification.Rd
tests/testdata/438-21-GEX/438-21-GEX.unknown.txt
tests/testdata/438-21-GEX/438-21-raw_feature_bc_matrix.h5
tests/testdata/438-21-GEX/read_count/barcodes.tsv.gz
tests/testdata/438-21-GEX/read_count/features.tsv.gz
tests/testdata/438-21-GEX/read_count/matrix.mtx.gz
tests/testdata/438-21-GEX/run_report.yaml
tests/testdata/438-21-GEX/umi_count/barcodes.tsv.gz
tests/testdata/438-21-GEX/umi_count/features.tsv.gz
tests/testdata/438-21-GEX/umi_count/matrix.mtx.gz
tests/testdata/438-21-GEX/validHashingBarcodes.csv
tests/testdata/438-24-GEX/438-24-GEX.unknown.txt
tests/testdata/438-24-GEX/run_report.yaml
tests/testdata/438-24-GEX/umi_count/barcodes.tsv.gz
tests/testdata/438-24-GEX/umi_count/features.tsv.gz
tests/testdata/438-24-GEX/umi_count/matrix.mtx.gz
tests/testdata/438-24-GEX/validHashingBarcodes.csv
tests/testdata/449-1-GEX/449-1-GEX.unknown.txt
tests/testdata/449-1-GEX/run_report.yaml
tests/testdata/449-1-GEX/umi_count/barcodes.tsv.gz
tests/testdata/449-1-GEX/umi_count/features.tsv.gz
tests/testdata/449-1-GEX/umi_count/matrix.mtx.gz
tests/testdata/449-1-GEX/validHashingBarcodes.csv
tests/testdata/457-1-GEX/457-1-GEX.unknown.txt
tests/testdata/457-1-GEX/run_report.yaml
tests/testdata/457-1-GEX/umi_count/barcodes.tsv.gz
tests/testdata/457-1-GEX/umi_count/features.tsv.gz
tests/testdata/457-1-GEX/umi_count/matrix.mtx.gz
tests/testdata/457-1-GEX/validHashingBarcodes.csv
tests/testdata/458-6-GEX.citeSeqCounts.2.citeseq/read_count/barcodes.tsv.gz
tests/testdata/458-6-GEX.citeSeqCounts.2.citeseq/read_count/features.tsv.gz
tests/testdata/458-6-GEX.citeSeqCounts.2.citeseq/read_count/matrix.mtx.gz
tests/testdata/458-6-GEX.citeSeqCounts.2.citeseq/umi_count/barcodes.tsv.gz
tests/testdata/458-6-GEX.citeSeqCounts.2.citeseq/umi_count/features.tsv.gz
tests/testdata/458-6-GEX.citeSeqCounts.2.citeseq/umi_count/matrix.mtx.gz
tests/testdata/471-1-GEX/471-1-GEX.unknown.txt
tests/testdata/471-1-GEX/run_report.yaml
tests/testdata/471-1-GEX/umi_count/barcodes.tsv.gz
tests/testdata/471-1-GEX/umi_count/features.tsv.gz
tests/testdata/471-1-GEX/umi_count/matrix.mtx.gz
tests/testdata/471-1-GEX/validHashingBarcodes.csv
tests/testdata/471-2-GEX/471-2-GEX.unknown.txt
tests/testdata/471-2-GEX/run_report.yaml
tests/testdata/471-2-GEX/umi_count/barcodes.tsv.gz
tests/testdata/471-2-GEX/umi_count/features.tsv.gz
tests/testdata/471-2-GEX/umi_count/matrix.mtx.gz
tests/testdata/471-2-GEX/validHashingBarcodes.csv
tests/testdata/483-3-GEX/483-3-GEX.unknown.txt
tests/testdata/483-3-GEX/run_report.yaml
tests/testdata/483-3-GEX/umi_count/barcodes.tsv.gz
tests/testdata/483-3-GEX/umi_count/features.tsv.gz
tests/testdata/483-3-GEX/umi_count/matrix.mtx.gz
tests/testdata/483-3-GEX/validHashingBarcodes.csv
tests/testdata/563-3-TCR.hashing.rawCounts.rds
tests/testdata/568-1-TCR.hashing.rawCounts.rds
tests/testdata/MS/cell_type_counts.csv
tests/testdata/allMsBarcodes.txt
tests/testdata/cellHashing/247-1-hashTagCounts.txt
tests/testdata/cellHashing/249-2-HTO_cellHashingRawCounts.txt
tests/testdata/cellHashing/282-1-HTO_cellHashingRawCounts.txt
tests/testdata/cellHashing/282-1-whitelist.txt
tests/testdata/cellHashing/283-cellbarcodeToHTO.calls.citeSeqCounts.txt
tests/testdata/cellHashing/283-validCellIndexes.csv
tests/testdata/cellHashing/umi_count/barcodes.tsv.gz
tests/testdata/cellHashing/umi_count/features.tsv.gz
tests/testdata/cellHashing/umi_count/matrix.mtx.gz
tests/testthat.R
tests/testthat/test-appendhashing.R
tests/testthat/test-bff.R
tests/testthat/test-cellhashing.R
tests/testthat/test-demuxem.R
tests/testthat/test-demuxmix.R
tests/testthat/test-gmmdemux.R
tests/testthat/testing-data.R
vignettes/.gitignore
vignettes/BFF-example_files/.DS_Store
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vignettes/BFF-example_files/figure-html/NormalizationQC-12.png
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vignettes/Benchmark-example_files/.DS_Store
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vignettes/V01-QC-example.Rmd
vignettes/V02-BFF-example.Rmd
vignettes/V03-Benchmark-example.Rmd
