Integrated Atlas: Myeloid Loading...
PCA by sample group
Customise sample groups
Gene expression
Select a gene to show its expression profile in the atlas
Benchmark another dataset using the atlas as a reference (vignette).
Project Stemformatics data
You can project any Stemformatics dataset onto this atlas. Select from the full list of datasets below. Start typing to quickly narrow down the choices. Go to search page and find the name if you want to use a more detailed search.
Project Other data
You can project your own bulk RNA-seq or microarray data. Select expression matrix and sample description files to upload. Both files need to be in tab separated format, with Ensembl gene ids or symbols as row ids and sample ids as column names. You can download example expression matrix and sample description files, if you want to examine the exact format.
Single cell data can be projected after pseudo-bulk aggregation. See the vignette for an example.
Capybara score
Once a projection has been made, you can see how the projected samples score against the atlas samples here as a heatmp using Capybara scores.
Extra tools for the atlas.
Download data
- samples matrix (~50kb)
- genes matrix (~360kb)
- expression matrix (226Mb)
- colours and ordering (1kb)
- pca coordinates (~50kb)
Stemformatics integrated atlas provides a way to visualise multiple datasets together. Read more about it at our about atlas page, which briefly outlines the method we used to construct the atlas and links to our published papers.
You can explore the atlas in several ways: "Sample groups" tab contains ways to view sample relationships, while "Gene expression" tab contains functions to plot gene expression in the atlas in different ways. In "Projection" tab, you'll find functions to project your own data onto the atlas for benchmarking cell types.
On the plots, zoom in or out using your mouse, double-click on individual samples in the PCA plot to see more information on their origin such as cell tye and sample description. All of the data and plots can be downloaded.
How to cite: see our cite page.