seqFISH | R Documentation |
seqFISH function assembles data on-the-fly from ExperimentHub
to provide a
MultiAssayExperiment
container. Actually the DataType
argument provides access to the
available datasets associated to the package.
seqFISH(
DataType = "mouse_visual_cortex",
modes = "*",
version,
dry.run = TRUE,
verbose = TRUE,
...
)
DataType |
|
modes |
|
version |
|
dry.run |
|
verbose |
|
... |
Additional arguments passed on to the ExperimentHub-class constructor |
seq FISH data are a combination of single cell spatial coordinates and transcriptomics for a few hundreds of genes. seq-FISH data can be combined for example with scRNA-seq data to unveil multiple aspects of cellular behaviour based on their spatial organization and transcription.
Available datasets are:
mouse_visual_cortex: combination of seq-FISH data as obtained from Zhu
et al. (2018) and scRNA-seq data as obtained from Tasic et al. (2016),
Version 1.0.0 returns the full scRNA-seq data matrix, while version 2.0.0
returns the processed and subsetted scRNA-seq data matrix (produced for
the Mathematical Frameworks for Integrative Analysis of Emerging
Biological Data Types 2020 Workshop) The returned seqFISH data are always
the processed ones for the same workshop. Additionally, cell types
annotations are available in the colData
through the class
column in
the seqFISH assay
.
scRNA_Counts - Tasic scRNA-seq gene count matrix
scRNA_Labels - Tasic scRNA-seq cell labels
seqFISH_Coordinates - Zhu seq-FISH spatial coordinates
seqFISH_Counts - Zhu seq-FISH gene counts matrix
seqFISH_Labels - Zhu seq-FISH cell labels
A
MultiAssayExperiment
of seq-FISH data
Dario Righelli <dario.righelli
seqFISH(DataType = "mouse_visual_cortex", modes = "*", version = "2.0.0",
dry.run = TRUE)
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