Repositories list

• notebook-projects

  Public
  Code for notebook project publishing and sharing

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• nbtools

  Public
  A framework for creating user-friendly widgets and tools in Jupyter

  nbextensionlabextensionpython+ 1jupyter

  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •4•18•1•0•Updated Oct 10, 2024Oct 10, 2024

• galahad

  Public
  Connect to the Galaxy platform within Jupyter notebooks.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

• ipyuploads

  Public
  A Jupyter file widget with improved upload capabilities

  pythonjupyterupload+ 1ipywidgets

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•1•0•Updated Oct 10, 2024Oct 10, 2024

• docs

  Public
  Documentation website for genomics 2 notebook (g2nb)

  1•0•0•0•Updated Jun 10, 2024Jun 10, 2024

• jupyter-wysiwyg

  Public
  A rich text editor for markdown cells in Jupyter

  wysiwyg-editornbextensionlabextension+ 1jupyter

  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •11•52•4•0•Updated Dec 11, 2023Dec 11, 2023

• website

  Public
  Temporary location of the website for testing

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

• hub-theme

  Public
  g2nb theme for JupyterHub

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

• visualizers

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Oct 27, 2023Oct 27, 2023

• jupyterlab-theme

  Public
  A theme extension for JupyterLab with the g2nb logo and colors

  CSS

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Oct 16, 2023Oct 16, 2023

• multiauthenticator

  Public
  Authenticate JupyterHub with multiple services

  jupyterhubauthenticator

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 7, 2023Aug 7, 2023

• guestauthenticator

  Public
  Sign in to JupyterHub using anonymous guest credentials

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 2, 2023Aug 2, 2023

• g2nb

  Public
  Meta-package for installing all of the g2nb tools

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•7•0•0•Updated Jul 24, 2023Jul 24, 2023

• cywidget

  Public
  A user-friend widget that accepts a Cytoscape file and visualizes the network

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Apr 18, 2023Apr 18, 2023

• fastawidget

  Public
  Widget that displays a FASTA file

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Feb 22, 2023Feb 22, 2023

• igv-jupyter

  Public
  Extension for Jupyter which integrates igv.js

  visualizationlabextensionjupyter

  JavaScript

  •

  MIT License

  •13•154•2•0•Updated Jan 3, 2023Jan 3, 2023

• tutorial-notebooks

  Public
  Jupyter notebooks for the g2nb project

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• Census-of-Immune-Cells-Single-Cell-Workflow-with-CoGAPS

  Public
  Demonstrates how to preprocess and analyze a large single-cell dataset, This version of the notebook includes all the Python and R code used for the analysis

  Jupyter Notebook

  •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• Genomic-Discovery-to-Translation

  Public
  Identify cancer subtype specific compounds using DiSCoVER (Hanaford et al, Clinical Cancer Research, 2016)

  Jupyter Notebook

  •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• ITCR2019-Drug-Recommendations-Using-DiSCoVER

  Public
  Notebook used for ITCR2019 by EFJ

  Jupyter Notebook

  •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• The-AMARETTO-framework-in-GenePattern-Notebook

  Public
  Multiscale and multimodal inference of regulatory networks to identify cell circuits and their drivers shared/distinct within/across biological systems of human disease, especially cancer

  Jupyter Notebook

  •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• Single-Cell-RNA-seq-Clustering-Analysis-Notebook

  Public
  Preprocessing and clustering for single cell RNA-seq data

  Jupyter Notebook

  •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• Cell-Migration-Quantification

  Public
  Quantify cell migration for circular migration regions

  Jupyter Notebook

  •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

• Methylation-Array-CNV-Analysis

  Public
  Perform Copy Number Variation Analysis on Illumina 450k/EPIC methylation array data.

  Jupyter Notebook

  •0•1•0•0•Updated Jan 21, 2022Jan 21, 2022

• Differential-expression

  Public
  Perform differential expression.

  Jupyter Notebook

  •0•0•0•0•Updated Jan 21, 2022Jan 21, 2022

• GenePattern-Notebook-Analysis-Template

  Public
  A best-practices template notebook for authoring GenePattern Notebook analyses.

  Jupyter Notebook

  •0•0•0•0•Updated Jan 21, 2022Jan 21, 2022

• volcano-plot

  Public
  Make a simple volcano plot

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 14, 2022Jan 14, 2022

• seurat-suite

  Public
  QC, preprocessing, clustering, and visualization of scRNA-seq data using Seurat.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 14, 2022Jan 14, 2022

• do-et-alli-20201

  Public
  Companion project to the publication A FZD7-specific antibody-drug conjugate induces solid tumor regression in preclinical models by Myan Do et al.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•3•0•0•Updated Jan 14, 2022Jan 14, 2022

• workshop-notebooks

  Public
  Jupyter notebooks intended for g2nb workshops

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jan 14, 2022Jan 14, 2022