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Add a single-cell data loader for tabular cell by gene matrices #1522

@arteymix

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@arteymix

This appears to be a typical output format for Smart-Seq and Drop-Seq workflows.

  • GSE142535 (Drop-Seq, series-level data)
  • GSE247340 (Drop-Seq, per-level)
  • GSE226938 (Smart-Seq, per-sample)
  • GSE237776 (InDrops, the format is a CSV instead of a TSV, per-sample)
  • GSE160519 (InDrops, same CSV format, per-sample)
  • GSE200942 (SureCell, CSV per-sample)
  • GSE230240 (InDrops, CSV per-sample)
  • GSE235987 (SMARTer scRNA-Seq, tabular, transposed, series-level data)

For some dataset, the data is provided at the series-level, we need a strategy for mapping column names (usually sample ID + barcode) to individual GEO samples. Fortunately, we already have implemented many approaches for that do deal with AnnData, although in this case, we might want something specialized that can also extract barcodes.

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