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Showing content from https://vsn-pipelines-examples.readthedocs.io/en/latest/ below:

VSN-Pipelines-examples — VSN-Pipelines-examples documentation

• 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.

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