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Experimental UMI counts and normalized data are available in the RNA assay. SCTransform-corrected count and log-normalized counts are available in the SCT assay. Please see the sctransform documentation for more details on this data. Predicted protein expression from the Seurat reference mapping procedure is stored in the predicted_ADT assay, and experimental protein expression for CITE-seq experiments is stored in the ADT assay. All metadata fields included with the original data are included, as well as standardized metadata, indicated with the “_standard” flag. More detailed information on these datasets, and processing code is available on github. Please see the SeuratDisk documentation for information on working with HDF5 files.\", \"columns\":[], \"files\":[ { \"name\":\"arunachalam_2020_processed.HDF5\", \"desc\":\"arunachalam\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/arunachalam_2020_processed.HDF5\", \"size\":\"2.78G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"bacher_2020_processed.HDF5\", \"desc\":\"bacher\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/bacher_2020_processed.HDF5\", \"size\":\"3.9G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"bost_2021_processed.HDF5\", \"desc\":\"bost\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/bost_2021_processed.HDF5\", \"size\":\"7.5G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"chua_2020_processed.HDF5\", \"desc\":\"chua\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/chua_2020_processed.HDF5\", \"size\":\"8.8G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"combes_2021_processed.HDF5\", \"desc\":\"combes\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/combes_2021_processed.HDF5\", \"size\":\"3.7G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"grant_2021_processed.HDF5\", \"desc\":\"grant\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/grant_2021_processed.HDF5\", \"size\":\"6.2G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"heming_2021_processed.HDF5\", \"desc\":\"heming\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/heming_2021_processed.HDF5\", \"size\":\"2.8G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"kusnadi_2021_processed.HDF5\", \"desc\":\"kusnadi\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/kusnadi_2021_processed.HDF5\", \"size\":\"2.8G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"lee_2020_processed.HDF5\", \"desc\":\"lee\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/lee_2020_processed.HDF5\", \"size\":\"3.07\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"liao_2020_processed.HDF5\", \"desc\":\"liao\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/liao_2020_processed.HDF5\", \"size\":\"4.09G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"meckiff_2020_processed.HDF5\", \"desc\":\"meckiff\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/meckiff_2020_processed.HDF5\", \"size\":\"6.47G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"schulte-schrepping_2020_processed.HDF5\", \"desc\":\"Schulte-Schrepping\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/schulte-schrepping_2020_processed.HDF5\", \"size\":\"13.6G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"silvin_2020_processed.HDF5\", \"desc\":\"silvin\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/silvin_2020_processed.HDF5\", \"size\":\"289M\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" },   { \"name\":\"stephenson_2021_processed.HDF5\", \"desc\":\"stephenson\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/stephenson_2021_processed.HDF5\", \"size\":\"27.4G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" },\n{ \"name\":\"su_2020_processed.HDF5\", \"desc\":\"su\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/su_2020_processed.HDF5\", \"size\":\"20.19G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"trump_2020_processed.HDF5\", \"desc\":\"trump\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/trump_2020_processed.HDF5\", \"size\":\"4.4G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"wen_2020_processed.HDF5\", \"desc\":\"wen\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/wen_2020_processed.HDF5\", \"size\":\"1.54G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"wilk_2020_processed.HDF5\", \"desc\":\"wilk\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/wilk_2020_processed.HDF5\", \"size\":\"1.63G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"yao_2021_processed.HDF5\", \"desc\":\"yao\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/yao_2021_processed.HDF5\", \"size\":\"2.4G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"yu_2020_processed.HDF5\", \"desc\":\"yu\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/yu_2020_processed.HDF5\", \"size\":\"10.71G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" }, { \"name\":\"zhu_2020_processed.HDF5\", \"desc\":\"zhu\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/zhu_2020_processed.HDF5\", \"size\":\"2.83G\", \"type\":\"HDF5\", \"date\":\"2019-12-01\" } ] }, { \"headline\":\"Merged Dataset\", \"desc\":\"Data from PBMC and whole blood (minus neutrophils and basophils) samples across all datasets, along with standard metadata, is available in the “merged” dataset as a SingleCellExperiment object. Transcriptomic data is saved as an HDF5 array to allow disk-backed interaction via the h5seuratArray R package. The download includes normalized transcriptomic data from the sctransform method. Predicted protein expression is included in the “altExp” slot. In addition to all metadata included here as visualization options, the download includes prediction scores for cell type annotations. The reference-mapped UMAP embeddings are available in the reducedDimensions, which is useful for visualization, as well as 50 components of cells mapped to the reference supervised PCA, which may be used for additional analysis.  \", \"columns\":[], \"files\":[ { \"name\":\"covid19_datasets.tar.gz\", \"desc\":\"merged dataset\", \"url\":\"https://atlas.fredhutch.org/data/hutch/covid19/downloads/covid19_datasets.tar.gz\", \"size\":\"46.2G\", \"type\":\"CDS\", \"date\":\"2019-12-01\" } ] } ] }"}]}}},"pageContext":{"id":"fc4606d9-fc57-52e4-a56e-cab916ef8c6b","cid":"436359cb-2391-57ee-8d31-d691fb5401b9"}},
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