The downstream analysis that I have done so far for the ebFRET data can be divided into the following questions:
1. What is the distribution of FRET values for each state that was identified by ebFRET?
ebFRET_HMM_State_Histograms.R 2. What is the idealized FRET efficiency for each FRET state that was identified by ebFRET?
FRET_Determination_ebFRET_v1.R 3. What is the actual FRET efficiency (non-idealized FRET) for each FRET state that was identified by ebFRET?
FRET_Determination_ebFRET(Actual FRET, Not Viterbi Mean).R 4. What is the lifetime of each FRET state that was identified by ebFRET? Outputs a file that can be used in MEMLET to determine rate constants for each state.
Rate_Determination_ebFRET_v2.R