seqFISH: Single-cell spatial + Gene Expression

In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

Single-cell spatial + Gene Expression

Description

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.

Usage

seqFISH(
  DataType = "mouse_visual_cortex",
  modes = "*",
  version,
  dry.run = TRUE,
  verbose = TRUE,
  ...
)

Arguments

DataType	character(1) indicating the identifier of the dataset to retrieve. (default "mouse_visual_cortex")
modes	character( ) The assay types or modes of data to obtain these include seq-FISH and scRNA-seq data by default.
version	character(1) Either version '1.0.0' or '2.0.0' depending on data version required (default '1.0.0'). See version section.
dry.run	logical(1) Whether to return the dataset names before actual download (default TRUE)
verbose	logical(1) Whether to show the dataset currently being (down)loaded (default TRUE)
...	Additional arguments passed on to the ExperimentHub-class constructor

Details

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

Value

A MultiAssayExperiment of seq-FISH data

Author(s)

Dario Righelli <dario.righelli <at> gmail.com>

Examples

seqFISH(DataType = "mouse_visual_cortex", modes = "*", version = "2.0.0",
    dry.run = TRUE)

waldronlab/SingleCellMultiModal documentation built on Nov. 3, 2024, 7:32 p.m.