### 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Links to older versions of the VoICE software that are no longer updated: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