GuibentifExtraData: Guibentif et al. accessory data

In MarioniLab/MouseGastrulationData: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis

Guibentif et al. accessory data

Description

Obtain the trajectory and NMP ordering data used in Guibentif et al.

Usage

GuibentifExtraData()

Details

This function downloads the data used in some of the analyses from Guibentif et al. (2020). Specifically, it contains the NMP cell orderings, and the atlas somitogenesis trajectory data.

This data is stored in a list. The first element of the list is named atlas_somite_trajectories, and is itelf a list that contains:

• masses:A data.frame containing the mass allocated to each cell from each trajectory (note: excluding extraembryonic, mixed_gastrulation timepoint, and doublet or stripped nuclei cells).

• membership:A data.frame containing the somite trajectory labels used in the paper, calculated from masses.

The second element is named nmp_orderings, and is also a list, which contains:

• atlas:A data.frame containing the position for each cell in the NMP ordering from the embryo atlas (see EmbryoAtlasData).

• wt_chimera:A data.frame containing the position for each cell in the NMP ordering from the WT chimera data (see WTChimeraData).

• t_chimera:A data.frame containing the position for each cell in the NMP ordering from the T chimera data (see TChimeraData).

Value

A list of the relevant somitogenesis trajectory and NMP ordering data will be returned. Details of the list structure are described in Details, below.

Author(s)

Jonathan Griffiths

References

Guibentif C, Griffiths JA et al. (2020). Title. Journal 566, 7745:490-495.

Examples

data <- GuibentifExtraData()

MarioniLab/MouseGastrulationData documentation built on Jan. 31, 2024, 11:01 a.m.