Welcome to cyclum-doc’s documentation!¶
Cyclum is a package that infer latent periodic process (e.g., cell cycle) from single-cell RNA-seq data. It provides methods to recover cell cycle information and remove cell cycle effects from the scRNA-seq data. The methodology projects high dimensional gene expression data to a circular manifold, instead of using marker genes.
We provide an Auto-Encoder based realization at this time, and we will add Gaussian Process Latent Variable Model soon. Also provided are a set of supplementary tools to visualize and anaylzing the result, in python and in R.