Oscope: a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq experiments

Ning Leng , Li-Fang Chu, Ron Stewart and Christina Kendziorski

University of Wisconsin Madison, Morgridge Institute for Research

Contact email: nleng@morgridge.org, kendzior@biostat.wisc.edu






Oscope is a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq experiments. Oscope capitalizes on the fact that cells from an unsynchronized population represent distinct states in a system. Oscope utilizes co-regulation information among oscillators to identify groups of putative oscillating genes, and then reconstructs the cyclic order of samples for each group, defined as the order that specifies each sample's position within one cycle of the oscillation, referred to as a base cycle. The reconstructed order is based on minimizing distance between each gene's expression and its gene-specific profile defined by the group's base cycle allowing for phase shifts between different genes.

Installation

Vignette

References

Updates

  • Latest updates could be found at NEWS on Bioconductor
  • 06/24/2015 Oscope 0.99.1 is available on Bioconductor now!
  • 06/24/2015 Oscope 0.0.6 is released