Introductory Videos

Getting help

SoS Notebook comes with an extensive set of documentation but it can be daunting to dive into it to get the information you need.

• If you have a casual question like if certain feature exists or how certain things are handled, it is better to ask it in our gitter channel. You can also use the button at the top right corner of the homepage.

• If you have a more serious question or suggestion, please feel free to post to our issue tracker. SoS consists of tens of modules and related issue trackers but free feel to post to any of them because it is easy for us to move the issue to an appropriate tracker if needed.

Documentation

Our documentation is hosted on our live server and can be edited directly. If you spot an error or feel like contributing to the document, please

1. Click the     button to the top right corner of each tutorial
2. Execute the notebook and edit it on our live server
3. Enter !create-pr <Shift-Enter> in the console panel to send us a PR

Using SoS Notebook

• Using multiple kernels in one Jupyter noetbook
• Working with arbitrary subkernels (magics %cd, %expand, %capture and %render)
• Exchanging data among kernels (magics %get, %put, %use, and %with)
• Using the console panel (console panel and shortcut Ctrl-Shift-Enter)
• Previewing variables and files (magic %preview)
• Tracking session and revision history of notebooks (magic %revisions and %sessioninfo)
• Running cell in modified environments (magic %env)
• Converting RMarkdown files to SoS notebooks (sos convert .rmd .ipynb)
• Exporting reports in HTML format (magic %convert)
• More on magic %use
• Workflow-execution magics (magics %run, %sosrun, %runfile)

Supported languages

• Working with Bash and Zsh (module sos-bash)
• Working with JavaScript and TypeScript (module sos-javascript)
• Working with Julia (module sos-julia)
• Working with Matlab and Octave (module sos-matlab)
• Working with Ruby (module sos-ruby)
• Working with Python 2 and Python3 (module sos-python)
• Working with R (module sos-r)
• Working with SAS (module sos-sas)
• Working with Scilab (module sos-scilab)
• Working with Stata (module sos-stata)
• Uisng the markdown kernel (module markdown-kernel)

Technical details

• SoS Magics
• Writing a new language module

Examples

Jupyter notebook to demonstrate features of SoS

• Types of cells (notebook)
  Demonstrate four types of cells that can be included in a Jupyter notebook
• DEG Annotation (notebook)
  An example to use Python to read an excel file, transfer the data to R, use R to translate ensembl gene IDs to HGNC gene names, then transfer data back to Python to write to a separate excel file
• Generation of reports with hidden details (notebook and generated report)
  This example demonstrates how to generate a report in HTML format with hidden details
• Use SAS with SoS (notebook)
  Simple examples on using SAS with SoS

Publications

Please cite the following publication if you use SoS Notebook for your work:

SoS Notebook: An Interactive Multi-Language Data Analysis Environment Bo Peng, Gao Wang, Jun Ma, Man Chong Leong, Chris Wakefield, James Melott, Yulun Chiu, Di Du, and John N. Weinstein, Bioinformatics, May 2018. doi: https://doi.org/10.1093/bioinformatics/bty405