SigProfilerExtractor 1.1.0

Install your desired reference genome from the command line/terminal as follows (available reference genomes are: GRCh37, GRCh38, mm9, and mm10):

This will install the human 37 assembly as a reference genome. You may install as many genomes as you wish.

Next, open a python interpreter and import the SigProfilerExtractor module. Please see the examples of the functions.

importdata Example

sigProfilerExtractor Example

sigProfilerExtractor Output

Estimation of the Optimum Solution Example

Estimation of the Optimum Solution Output

The files below will be generated in the output folder: | File Name | Description | | ----- | ----- | | All_solutions_stat.csv | A csv file that contains the statistics of all solutions. | | selection_plot.pdf | A plot that depict the Stability and Mean Sample Cosine Distance for different solutions. |

Decompose Example

Decompose Output

Values: The files below will be generated in the output folder:

• Cluster_of_Samples.txt
• comparison_with_global_ID_signatures.csv
• Decomposed_Solution_Activities.txt
• Decomposed_Solution_Samples_stats.txt
• Decomposed_Solution_Signatures.txt
• decomposition_logfile.txt
• dendogram.pdf
• Mutation_Probabilities.txt
• Signature_assaignment_logfile.txt
• Signature_plot[MutatutionContext]_plots_Decomposed_Solution.pdf

Activity Stacked Bar Plot Example

GPU support

If CUDA out of memory exceptions occur, it will be necessary to reduce the number of CPU processes used (the ^{} parameter).