burstH2MM documentation

burstH2MM is designed to make analyzing single molecule burst experiments with H²MM easy. burstH2MM is built to work with FRETBursts, on which it depends for burst search and selection. burstH2MM serves to organize and process the results of H²MM optimizations and access the results of Viterbi analysis, which assigns each photon a state, and further processing segments the data into dwells.

Installation

To install burstH2MM simply type

pip install burstH2MM

into your terminal window. Python 3.8 or greater is required.

Please Cite

H²MM was originally introduced by Pirchi and Tsukanov et. al. 2016 and this implementation is built on the extension introduced in Harris et. al. 2022. If you use this library in a publication, please make sure to cite both these papers.

Contents

Contents:

• Tutorial
  • H²MM analysis
  • Uncertainty Estimation
  • Boostrap Uncertainty
• Divisor Approach
• How To Guides
  • Controlling Plotting Functions
  • Accessing the Results of an Optimization
  • Quantifying Accuracy/Precision of Model Parameter Values
  • Using \(\mu\)sALEX
  • Access Divisors and Models
  • Customization and Control
  • Caclulating Nanotimes with Confidence Threshold
  • Simulations
• Discussion
  • What is H²MM?
  • A Brief History of H²MM
  • Data organization
  • Divisors
• Documentation
  • BurstSort
  • Plotting
  • Selections
  • Uncertainties
  • Simulations
• Examples of Full Data Analysis
  • Hairpin 3 in 300 mM NaCl, nsALEX

Indices and tables

• Index

• Module Index

• Search Page

Thank you for using H²MM