Skip to main content
Ctrl+K

KSTAR 1.1.0 documentation

Overview:

  • Overview
  • Dependencies
  • Preparing your Data
  • Options for Running KSTAR

Galaxy Tutorial:

  • Run KSTAR on Galaxy
  • Analyze Results

Python Tutorial (Just the Basics):

  • Getting Started
  • Map Dataset to Reference
  • Predict Kinase Activities
  • Plotting/Analysis
    • Summary PDFs
    • DotPlots
    • Additional Analyses

Example Vignettes:

  • Analysis Examples
    • EGF Stimulation of 184A1 Cells (Wolf Yadlin, 2007)
    • EGF and HRG Stimulation of ERBB2 Overexpressing HMEC Cells (Wolf Yadlin 2006)
    • TCR Activation (Chylek, 2014)
    • BCR-ABL inhibition by dasatinib in K562 cells (Asmussen, 2014)
    • Inhibition of AKT by Five Different Inhibitors in Breast Cancer (Weichmann, 2021)
    • Paradoxical Activation of MAP-ERK pathway upon BRAF inhibition (Kubiniok, 2017)
    • Analysis of CPTAC Breast Cancer Patient Samples (Mertens 2016)
    • Analysis of PDX Tumor Samples (Huang 2017)
    • Analysis of HER2 Positive Patients using Microbiopsies (Satpathy 2021)

Advanced Python Usage:

  • KSTAR Reference
  • Updating Configuration
  • Network Generation
  • Pregenerated Random actiivities
  • KSTAR in Parallel
  • Frequently Asked Questions
  • Repository
  • Open issue

Python Module Index

k
 
k
- kstar
    kstar.analysis.coverage
    kstar.analysis.interactions
    kstar.analysis.kinase_MI
    kstar.calculate
    kstar.config
    kstar.dataset_processing.accessions
    kstar.dataset_processing.peptides
    kstar.helpers
    kstar.prune

By Naegle Lab

© Copyright 2020, Naegle Lab.