Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and Antibody-Derived Tags (ADTs) using the 10X 3' Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0.All files stored in this entry are from sample 4 donor 8. Additional sample are available upon request.File descriptionfiltered_feature_bc_matrix.h5: Filtered feature-barcode matrix containing only detected cell-associated barcodes.raw_feature_bc_matrix.h5: Unfiltered feature-barcode matrix containing every barcode from the list of barcode sequences with at least one read, including background and cell-associated barcodes.CitationLuecken, M. D. et al. A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track (2021).Original data linkhttps://openproblems.bio/neurips_docs/data/dataset/

Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and Antibody-Derived Tags (ADTs) using the 10X 3' Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0.File Descriptioncite_quality_control.h5mu: Filtered cell by feature MuData object after quality control.cite_normalization.h5mu: MuData object of normalized data using DSB (denoised and scaled by background) normalization.cite_doublet_removal_xdbt.h5mu: MuData of data after doublet removal based on known cell type markers. Cells were removed if they were double positive for mutually exclusive markers with a DSB value >2.5.cite_dimensionality_reduction.h5mu: MuData of data after dimensionality reduction.cite_batch_correction.h5mu: MuData of data after batch correction.CitationLuecken, M. D. et al. A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track (2021).Original data linkhttps://openproblems.bio/neurips_docs/data/dataset/

Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and Antibody-Derived Tags (ADTs) using the 10X 3' Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0.File Descriptioncite_filtered.h5mu: Filtered barcode by feature MuData object of concatenated donor’s raw counts from filtered barcodes. This is built from the Cell Ranger output and contains the RNA and ADT ("prot" key) data.cite_raw.h5mu: Unfiltered barcode by feature MuData object of concatenated donor's raw counts extracted by Cell Ranger. It contains the RNA and ADT ("prot" key) data.cite_preprocessed.h5ad: Fully processed AnnData object used in annotation chapter.CitationLuecken, M. D. et al. A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track (2021).Original data linkhttps://openproblems.bio/neurips_docs/data/dataset/