ABseq App

A resource of gene and surface protein expression in human bone marrow
Citation: Triana S, Vonficht D, Jopp-Saile L, et al. Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states. bioRxiv; 2021. DOI: 10.1101/2021.03.18.435922.

Contact: Sergio Triana, at EMBL Heidelberg, Haas Lab at DKFZ, HI-STEM, BIH, Charité and BIMSB-MDC and Velten lab at CRG

Please use Google Chrome when running the app and wait a couple of minutes while the data loads, in the meantime you can check the following tutorial video.

MOFA-UMAP
This UMAP was calculated using the MOFA dimensions obtained from the antibody and RNA layers

            
Volcano Plot
Differential expression result
Here you can modify the threshold used for every antibody. The default value is the OTSU calculated threshold. These thresholds are used for the calculation of gating schemes using the `tree based` method in the `Calculate scheme` tab and the scheme option in the `Visualisation` tab
Please select either, the Hypergate algorithm by Becht et al., 2019 or (Tree Based) a decision three approach using OTSU calculated thresholds, (Tree Based Manual) a tree based approach using the threshold modified by yourself in the `threshold` tab or (Tree based Continous) a tree based approach where the tree algoritm selects the thresholds

MOFA-UMAP
This UMAP was calculated using the MOFA dimensions obtained from the antibody and RNA layers
Fate Bias
This plot show the fate bias of the selected trajectory
Expression in the pseudotime
These plots show the expression of a feature throught the pseudotime of each trajectory