Skip to content

README.md

Latest commit

 

History

History
49 lines (33 loc) · 1.88 KB

README.md

File metadata and controls

49 lines (33 loc) · 1.88 KB

Layer Annotation Validation

This folder contains scripts and outputs for validating cortical layer marker genes across species.

Files and Directories

  • validate_layer_annotation.ipynb
    Notebook that computes and plots correlation of layer markers within and between species.

  • visualise_selected_markers.ipynb
    Notebook that visualizes selected marker genes on Visium spatial slides across species.

  • adults/, chimp/, human/, macaque/
    Subfolders with species-specific DE analysis results and figures (see their individual README.md files).

  • figures/
    Contains correlation heatmap images across species:

    • inspecie_correlation.jpg
      Shows the correlation of marker gene sets for each species against itself (intra-species marker consistency).
    • adults_correlation.jpg
      Shows how adult human (spatialLIBD) marker genes correlate with marker genes from each other species.
    • newbornhuman_correlation.jpg
      Shows how marker genes identified in newborn human samples correlate with markers in each other species.

Figure Previews

Intra-species Marker Correlation

Intra-species correlation

This heatmap plots the Pearson correlation of significant layer marker gene sets within each species.

Adult vs. Other Species Correlation

Adult vs other species correlation

Correlation of adult human marker gene sets against those from human newborn, chimpanzee, and macaque.

Newborn Human vs. Other Species Correlation

Newborn human vs other species correlation

Correlation of newborn human marker gene sets against those from chimpanzee, macaque, and adult human samples.