Quick Start Guide

Call from bash

The easiest way to run Cyclum as a stand alone software. The expression of mESC in TPM is provided in the data directory. Just make sure you have all the dependencies and cd to the folder containing run_cyclum.py and run

$ python run_cyclum.py data/mESC/mesc-tpm.csv --cell-is-column --remove

You will find the outputs in the same directory as the input file data/mESC/. mesc-tpm-cell.csv contains the pseudotime for all cells. mesc-tpm-gene.csv contains the “magnitude” and “phase” of the cell-cycle components in the genes. mesc-tpm-corrected.csv contains the expression matrix with cell-cycle component removed.

Call from python

Nonetheless, Cyclum is also a python package. We provide examples for recovering cell cycle and removing cell cycle by calling it in python. Please click on the following links to access them.

• Recover cell cycle in mESC
• Remove cell cycle from perturbed mESC
• Analyze Melanoma Patient 78
• mESC analysis using the object oriented core