<jupyter_start><jupyter_text>GenePattern Notebook Analysis Template **Author** - <NAME>**Email** - <EMAIL>This notebook performs ____ analysis. Provide references[[1]](http://www.pnas.org/content/102/43/15545.short) in this section as appropriate. Number in same order as references are listed at the end of the notebook. SummaryThe goal of this notebook is ... Briefly describe the biological objective of this analysis. Provide references for packages (Python, R, cmd line tool, etc.) used as appropriate. Use CaseDescribe the example data being used and the biological signifiance of this analysis. DatasetDescribe the technical aspects of the example dataset used in the analysis along with links to where to find the original data if possible (e.g. GEO, TCGA, etc.). Analysis OverviewMake a copy of this [template](https://docs.google.com/presentation/d/1atuIavj7fzdLeqJs36fOXvi9pPT7KMOZpib24m0J06g/editslide=id.g3973a57c63_0_68) to create a workflow diagram. Export the diagram as a `png` file and drag it into this markdown cell.![gp_notebook_workflow_template.png](attachment:gp_notebook_workflow_template.png) Table of Contents1. **[Preprocess Data](Step-1:-Preprocess-Data)**    1. Load the dataset and perform preprocessing.    2. ...2. **[...](Step-2:-...)**  Login to GenePattern Login to a GenePattern server to perform the following analyses.**NOTE:** This can be removed if the notebook only uses UI Builder cells.<jupyter_code># Requires GenePattern Notebook: pip install genepattern-notebook
import gp
import genepattern

# Username and password removed for security reasons.
genepattern.GPAuthWidget(genepattern.register_session("https://gp-beta-ami.genepattern.org/gp", "", ""))<jupyter_output><empty_output><jupyter_text>Step 1: Preprocess Data This step performs... Briefly describe what each analysis step does, especially if multiple transformations are performed. Instructions     Load data in **dataset** parameter.    Set parameter **xxx** to `value`.**Estimated run time**: ~ 5 minutes, ~ 30 minutes, ~ 1 hour, etc.**Input files**Describe formatting of input files or link to the appropriate file format description provided [here](http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide).**Output files**- `output1.txt` - describe contents of first output file- `output2.txt` - describe contents of second output file<jupyter_code># GenePattern Analysis Cell<jupyter_output><empty_output><jupyter_text>Step 2: ... This step performs.... (1-2 sentences) Instructions **Supported file formats**: `txt`, and `gct`.    Load data in **dataset** parameter.    Set parameter **xxx** to `value`.**Estimated run time**: ~ 5 minutes, 30 minutes, ~ 1 hour, etc.**Output files**- `output1.txt` - describe contents of first output file- `output2.txt` - describe contents of second output file<jupyter_code># GenePattern Analysis Cell<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.10395869191049914, 'fraction_numerical': 0.0189328743545611, 'mean_word_length': 5.37280701754386, 'pattern_counts': {'":': 0, '<': 15, '<?xml version=': 0, '>': 15, 'https://': 2, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '3', 'dir': 'jupyter-structured-clean-dedup', 'id': '539432', 'license': 'MIT', 'n_tokens_mistral': 837, 'n_tokens_neox': 790, 'n_words': 307, 'path': 'GenePattern Notebook Analysis Template.ipynb', 'repo_name': 'genepattern/gp-notebook-template', 'size': '2918'}