VoICE – Vocal Inventory Clustering Engine
All code here written by Zachary Burkett and Nancy Day. All code here is provided as is. Any revisions to the code will be posted with a date.
13 May 2015 – edits to R files for updated WGCNA package
See these GitHub pages for tutorials on the use of VoICE:
Links to older versions of the VoICE software that are no longer updated:
MATLAB code for song sequence analysis, resampling statistics, and microarray pre-processing
All code here written by Austin Hilliard. Anyone is free to use/re-use any of it, however, ATH offers absolutely no warranty and cannot guarantee it will work as intended on your particular system. Dependencies are noted or provided when possible.
R CODE RELATED TO MICROARRAY ANALYSIS:
Example code exploring Supp. Table S2 from Hilliard et al., 2012… search_examples.R
Pre-processing functions for removing outlier probes and samples, and normalizing… micorarray_preprocessing.R
AUSTIN’S MATLAB / RESAMPLING TUTORIALS:
Session 1 (1/15/09): Powerpoint
Session 2 (1/22/09): Powerpoint (Incomplete, see Session 3)
Session 3 (1/29/09): Powerpoint + Code for transition probability + Example data
Session 4 (2/5/09): Powerpoint + Code comparing means of 2 independent datasets
Session 5 (2/12/09): Powerpoint + Better version of code to compare 2 independent datasets; more descriptive help file, checks user input, outputs struct, can demo using randomly generated data
Session 6 (2/19/09): Powerpoint
Resampling code for comparing 2 dependent (paired) datasets
All MATLAB resampling functions on this page require at least one of sample.m, proportion.m and/or count.m from Daniel Kaplan’s resampling toolbox
SONG SEQUENCE MATLAB FUNCTIONS:
Compute transition probability from leading to following syllable, and to the end of a motif… m-file
Compute transition probability matrix of dataset. Rows represent leading syllables, columns represent following syllables, e.g. the entry at position (3,2) is the probability that syllable 3 will be followed by syllable 2. The final column represents the probability of that leading syllable ending the motif… m-file
