- Analysis of 10k PBMCs from a single healthy human donor (10x Genomics): Includes standard "best practices" analysis alongside SCENIC gene regulatory network inference.
SCENIC multi-runs
- Analysis of 10k PBMCs with multiple SCENIC iterations (10x Genomics): Includes standard "best practices" analysis alongside SCENIC gene regulatory network inference.
- Analysis of multiple samples in the adult Drosophila midgut (Hung, R.-J. et al., 2019):
- Obtain expression counts, combine samples, apply BBKNN batch correction, then run SCENIC gene regulatory inference.
- Obtain expression counts, combine samples, apply Harmony batch correction, then append SCENIC results from the BBKNN run.
- Analysis of multiple samples in the adult Drosophila ageing brain (Davie, K., Janssens, J., Koldere, D. et al., 2018):
- Obtain expression counts, combine samples, apply BBKNN batch correction, then run SCENIC gene regulatory inference.
- Obtain expression counts, combine samples, apply Harmony batch correction, then append SCENIC results from the BBKNN run.
- Analysis of multiple samples in the third instar female larvae Drosophila wing disc (Bageritz, J., Willnow, P., Valentini, E. et al., 2019):
- Obtain expression counts, combine samples, apply BBKNN batch correction, then run SCENIC gene regulatory inference.
- Obtain expression counts, combine samples, apply Harmony batch correction, then append SCENIC results from the BBKNN run.
- Analysis of multiple samples in the Drosophila brain: (Kurmangaliyev et al., 2019):
- Obtain expression counts, combine samples, apply BBKNN batch correction, then run SCENIC gene regulatory inference.
- Obtain expression counts, combine samples, apply Harmony batch correction, then append SCENIC results from the BBKNN run.
- Analysis of multiple samples in the third instar female larvae Drosophila Enteroendocrine Cells (Guo, X. et al., 2019):
- Obtain expression counts, combine samples, apply BBKNN batch correction, then run SCENIC gene regulatory inference.
- Obtain expression counts, combine samples, apply Harmony batch correction, then append SCENIC results from the BBKNN run.
- Analysis of multiple samples in the Drosophila scribble mutant tumors (Ji, T., et al., 2019):
- Obtain expression counts, combine samples, apply BBKNN batch correction, then run SCENIC gene regulatory inference.
- Obtain expression counts, combine samples, apply Harmony batch correction, then append SCENIC results from the BBKNN run.
- Analysis of multiple samples in the Drosophila larval brain (Brunet Avalos, C. et al., 2019):
- Obtain expression counts, combine samples, apply BBKNN batch correction, then run SCENIC gene regulatory inference.
- Obtain expression counts, combine samples, apply Harmony batch correction, then append SCENIC results from the BBKNN run.