Welcome to MutaGene’s documentation!¶
What is MutaGene?¶
MutaGene is a set of methods for the analysis of mutations and mutational processes in cancer. The MutaGene Python package consists of command-line tools that provide direct access to some of the functions available on MutaGene’s website.
The MutaGene software package includes 5 subpackages: fetch, profile, rank, motif, and signature. Each subpackage has a unique functionality.
What are MutaGene’s five subpackages?¶
How can I install and use MutaGene?¶
Installation: MutaGene package is accessible via standard python repository PyPi. The package requires Python3.6 or higher.
Usage: The MutaGene package can be ran on the command line.
Here are detailed instructions to install and use MutaGene. - add links to command-line MutaGene documentation and, of course, subpackages
How can I cite MutaGene?¶
If you use MutaGene, you should cite:
Goncearenco A, Rager SL, Li M, Sang Q, Rogozin IB, Panchenko AR Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Res. 2017; 45(W1):W514–W522. https://doi.org/10.1093/nar/gkx367
Additionally, if you use the MutaGene rank subpackage, you should cite the driver prediction method as:
Brown AL, Li M, Goncearenco A, Panchenko AR Finding driver mutations in cancer: Elucidating the role of background mutational processes. PLOS Computational Biology 2019; 15(4): e1006981. https://doi.org/10.1371/journal.pcbi.1006981