The jPCA MATLAB code pack, including examples, can be downloaded from Professor Mark Churchland's lab website Movement Generation Lab (see under "links") or Professor John Cunningham's lab website Cunningham Lab (see under "publications"). jPCA was introduced in: Churchland MM*, Cunningham JP*, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV (2012) Neural population dynamics during reaching. Nature. 487:51-56.
Matt Kaufman, during his graduate work, Iwrote a spike-sorting program in Matlab called MKsort. It is now distributed by Ripple LLC, free and open-source. It is targeted mainly at use with Utah arrays, but can be used with other systems as well. It is presently considered "in beta", but is quite stable and has been in use by the Shenoy lab for several years. It can be downloaded from Matt Kaufman's website: MKsort
The Variance MATLAB code pack, including examples, can be downloaded from Professor Mark Churchland's lab website Movement Generation Lab (see under "links"). Variance (FF with 'mean matching') was introduced in: Churchland MM*, Yu BM*, Cunningham JP, Sugrue LP, Cohen MR, Corrado GS, Newsome WT, Clark AM, Hosseini P, Scott BB, Bradley DC, Smith MA, Kohn A, Movshon JA, Armstrong KM, Moore T, Chang SW, Snyder LH, Lisberger SG, Priebe NJ, Finn IM, Ferster D, Ryu SI, Santhanam G, Sahani M, Shenoy KV (2010) Stimulus onset quenches neural variability: a widespread cortical phenomenon. Nature Neuroscience. 13:369-378.
The GPFA MATLAB code pack, including examples, can be downloaded from Professor Byron Yu's lab website Yu Lab(see under "software"). GPFA was introduced in: Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV*, Sahani M* (2009) Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity. Journal of Neurophysiology. 102:614-635.