humanHippocampus2024 - Access to SRT and snRNA-seq data from spatial_HPC project
This is an ExperimentHub Data package that helps to access the spatially-resolved transcriptomics and single-nucleus RNA sequencing data. The datasets are generated from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. The datasets are based on [spatial_hpc](https://github.com/LieberInstitute/spatial_hpc) project by Lieber Institute for Brain Development (LIBD) researchers and collaborators.
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experimenthubsequencingdataspatialdataexpressiondatatissuernaseqdatadatapkg
6.00 score 10 stars 9 scriptsBatchSVG - Identify Batch-Biased Spatially Variable Genes
BatchSVG is a method to identify batch-biased spatially variable genes (SVGs) in spatial transcriptomics data. The batch variable can be defined as sample, donor sex, or other batch effects of interest. The BatchSVG method is based on the binomial deviance model (Townes et al, 2019).
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spatialtranscriptomicsbatcheffectqualitycontrolbatch-effectbioconductor-packagespatial-transcriptomics
5.47 score 5 stars 13 scripts 269 downloadsHuBMAPR - Interface to 'HuBMAP'
'HuBMAP' provides an open, global bio-molecular atlas of the human body at the cellular level. The `datasets()`, `samples()`, `donors()`, `publications()`, and `collections()` functions retrieves the information for each of these entity types. `*_details()` are available for individual entries of each entity type. `*_derived()` are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using `bulk_data_transfer()`.
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softwaresinglecelldataimportthirdpartyclientspatialinfrastructurebioconductor-packageclienthubmaprstudio
5.35 score 3 stars 289 downloads