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.

Contents:

• Quick Start Guide
  • Notebooks
  • Call from python
  • Tranferring data from/to R and to GSEA
• cyclum2
  • cyclum package
• FAQ
  • What preprocess should be done on the scRNA-seq data?
  • How do I choose number of linear dimensions?
  • What does the pseudo-time mean?
  • What does the circular pseudo-time mean?
• License

Indices and tables

• Index

• Module Index

• Search Page