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spatialdatasets's Introduction

SpatialDatasets

The SpatialDatasets package contains a collection of spatially-resolved omics datasets, which have been formatted into the SpatialExperiment, MoleculeExperiment or CytoImageList Bioconductor classes, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms including IMC, MIBI-TOF, Xenium, CosMx and MERFISH. They have been sourced from various publicly available sources.

spatialdatasets's People

Contributors

ellispatrick avatar alexrunqin avatar fame2827 avatar

Watchers

Dario Strbenac avatar Garth Tarr avatar John Ormerod avatar avatar CSB Yang Laboratory avatar Samuel Muller avatar Shila Ghazanfar avatar Nick R. avatar

spatialdatasets's Issues

make keren data script error

The script needs revision. It lacks

library(BiocParallel)
library(tidyr)
library(readr)
library(tibble)

and it fails at

patientData = patientData %>%

  • rename(V1 = "patient",
  •      V2 = "tumour_type") %>%
  • mutate(tumour_type = case_when(tumour_type == 0 ~ " ..." ... [TRUNCATED]
    Error in rename():
    ! Can't rename columns that don't exist.
    ✖ Column patient doesn't exist.

More importantly -- is there any workflow associated with the Keren spe object? I looked
at the tiff files and they are mostly black ... I applied to get the ionpath viewer access. Am
I missing some documentation on what to do with this dataset? I confess that I haven't read
the paper yet ...

Thanks

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