### Download Example Data

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/2. Quick Start Example.md

Command to download the example dataset '21BRCA.zip' using wget.

```bash
$ wget ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerExtractor/Example_data/21BRCA.zip
```

--------------------------------

### Running SigProfilerExtractor (Matrix)

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/2. Quick Start Example.md

Python commands to import SigProfilerExtractor and run the extraction with matrix input.

```python
>>> from SigProfilerExtractor import sigpro as sig
>>> sig.sigProfilerExtractor("matrix", "results", "path/to/21BRCA.txt", reference_genome="GRCh37", minimum_signatures=1, maximum_signatures=10, nmf_replicates=100, cpu=-1)
```

--------------------------------

### Running SigProfilerExtractor (VCF)

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/2. Quick Start Example.md

Python commands to import SigProfilerExtractor and run the extraction with VCF input.

```python
>>> from SigProfilerExtractor import sigpro as sig
>>> sig.sigProfilerExtractor("vcf", "results", "path/to/21BRCA_vcf", genome_build="GRCh37", minimum_signatures=1, maximum_signatures=10, nmf_replicates=100)
```

--------------------------------

### Install from PyPI

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/wikies/Installation.md

Install SigProfilerExtractor using pip.

```bash
pip install SigProfilerExtractor
```

--------------------------------

### Install from source

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/wikies/Installation.md

Clone the repository and install SigProfilerExtractor from source.

```bash
git clone https://github.com/SigProfilerSuite/SigProfilerExtractor.git
cd SigProfilerExtractor
pip install .
```

--------------------------------

### Install reference genomes

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/wikies/Installation.md

Install at least one reference genome using SigProfilerMatrixGenerator.

```python
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install("GRCh37")
```

--------------------------------

### Example: Matrix Input

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/wikies/CLI-Usage.md

An example of using SigProfilerExtractor with matrix input data.

```bash
SigProfilerExtractor sigprofilerextractor matrix example_output /path/to/Samples_SBS.txt --minimum_signatures 1 --maximum_signatures 3
```

--------------------------------

### Mac/Unix Github Release Installation - Install Package

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/1. Installation.md

Installs SigProfilerExtractor from the cloned Github repository on Mac/Unix systems.

```bash
cd SigProfilerExtractor 
pip install .
```

--------------------------------

### Import Example Data

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/README.md

Imports the path of example data.

```python
importdata(datatype="matrix")
```

--------------------------------

### Mac/Unix Github Release Installation - Clone Repository

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/1. Installation.md

Clones the SigProfilerExtractor Github repository for installation from source on Mac/Unix systems.

```bash
git clone git@github.com:AlexandrovLab/SigProfilerExtractor.git
```

--------------------------------

### Install SigProfilerExtractor from GitHub

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/README.md

To install the current version of this Github repo, git clone this repo or download the zip file. Unzip the contents of SigProfilerExtractor-master.zip or the zip file of a corresponding branch. In the command line, please run the following:

```bash
cd SigProfilerExtractor-master
pip install .
```

--------------------------------

### Estimation of the Optimum Solution Example

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/README.md

An example demonstrating how to call the estimate_solution function to find the optimal number of signatures.

```python
from SigProfilerExtractor import estimate_best_solution as ebs
ebs.estimate_solution(base_csvfile="All_solutions_stat.csv", 
          All_solution="All_Solutions", 
          genomes="Samples.txt", 
          output="results", 
          title="Selection_Plot",
          stability=0.8, 
          min_stability=0.2, 
          combined_stability=1.0,
          allow_stability_drop=False,
          exome=False)
```

--------------------------------

### Import Example Data

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/3. Using the Tool - Input.md

Import example data using the importdata function, specifying the desired data type.

```python
data = sig.importdata(datatype)
```

--------------------------------

### Activity Stacked Bar Plot Example

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/README.md

Command-line example for generating an activity stacked bar plot.

```bash
$ python plotActivity.py 50 sig_attribution_sample.txt test_out.pdf
```

--------------------------------

### Example: VCF Input

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/wikies/CLI-Usage.md

An example of using SigProfilerExtractor with VCF input data, specifying a reference genome.

```bash
SigProfilerExtractor sigprofilerextractor vcf example_output /path/to/vcf_folder --reference_genome GRCh37 --minimum_signatures 1 --maximum_signatures 3
```

--------------------------------

### Install Reference Genome

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/README.md

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

```python
python
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh37')
```

--------------------------------

### Get help on sigProfilerExtractor parameters

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/3. Using the Tool - Input.md

This command displays detailed help information for the sigProfilerExtractor function, including its parameters and outputs.

```python
help(sig.sigProfilerExtractor)
```

--------------------------------

### importdata Example

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/README.md

This "data" variable can be used as a parameter of the "project" argument of the sigProfilerExtractor function.
To get help on the parameters and outputs of the "importdata" function, please use the following:

```python
from SigProfilerExtractor import sigpro as sig
path_to_example_table = sig.importdata("matrix")
data = path_to_example_table 
# This "data" variable can be used as a parameter of the "project" argument of the sigProfilerExtractor function.

# To get help on the parameters and outputs of the "importdata" function, please use the following:
help(sig.importdata)
```

--------------------------------

### Help Command

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/wikies/CLI-Usage.md

Command to display all available flags and options for SigProfilerExtractor.

```bash
SigProfilerExtractor sigprofilerextractor --help
```

--------------------------------

### Running estimate_best_solution

Source: https://github.com/sigprofilersuite/sigprofilerextractor/blob/master/docs/3. Using the Tool - Input.md

Shows how to call the estimate_solution function to estimate the optimum solution.

```python
ebs.estimate_solution()
```