Epilepsy19

Analysis for the Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis paper.

To see the compiled notebooks, please visit the website.

Interactive data exploration

• Conos alignment (con_filt_cells)
• Conos alignment with bad samples removed (con_filt_samples)
• By sample
  • Control: C1, C2, C3, C4, C5, C6, C7, C8, C9, C10
  • Epilepsy: E1, E2, E3, E4, E5, E6, E7, E8, E9

*See the demonstration for Pagoda 2 web apps

The raw notebooks

• Pre-processing
  • Raw data filtering
  • Alignment of the datasets
• Analyses
  • Overview of the datasets
  • Distances between cell types
  • Differential Expression and Gene Ontology analyses
  • Cell Type prioritization summary
  • Comparison to Smart-Seq2 and Allen Brain Institute data
  • Gene module analysis

Data, used for analysis

You can find all data files with download guides here: http://kkh.bric.ku.dk/Epilepsy19/

Conos objects and filtered count matrices (must be saved into the cache folder):

• [con_filt_cells.rds] alignment of all neuronal cells
• [con_filt_samples.rds]: 3 bad samples removed from the analysis
• [count_matrices.rds]: filtered count matrices

Additional data:

• [cms_raw.rds]: raw count matrices (as they were loaded in chunks 2 and 5 of the pre-processing notebook)

Relevant meta-data:

• CellAnnotatoR-compatible list of marker genes
• Cell type annotation
• Sample information

Citation

If you used this code for your analysis, please cite the paper:

Pfisterer, U., Petukhov, V., Demharter, S. et al. Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis. Nat Commun 11, 5038 (2020). https://doi.org/10.1038/s41467-020-18752-7