SynapticSage

CoNNECT

(ryoung mod, GPU version) CoNNECT: Convolutional Neural Network for Estimating synaptic Connectivity from spike Trains. Endo et al., bioRxiv (2020).

mlab-utils

(🌌🔍 Vastly simplifies working with filter-framework datafiles...📂💡) Collection of core tools I've built to deal with fillter framework and nd branched cell types in JLab.

Neural_Realime-ClosedLoop-PhaseDisruption

ryoung's closed loop module for real-time detection of theta (or beta) phase and triggering optogenetic disruption using the SpikeGadgets software environment (https://spikegadgets.com/)

2022-LISH-Harvard-DatascienceCompetition

Lab for Innovation Science at Harvard data science competition. My solution scored around the top 15. I had planned to try other things, but I used only 1/3 of the allowed competition time -- and hence did not explore advanced feature engineering in the winning solutions. But interestingly, this solution was similar to winning solutions.

Bettermarks

Bookmarking system for Bash and Zsh

config

git control of my key configuration files (neovim, spacemacs, and tmux)

GoalFetchTask-AnalysisTools

List of scripts and functions used to pry future-past related codes in the HPC-PFC system

mountainsort-2-phy

Converts moutainsorted clusters to phy for curation using SpikeInterface. Includes a plugin to add mountainsort cluster metrics to phy.

MuseEEGHeadset-Scrubber

Scrubs data from Muse EEG headset into a Tidy Data format. https://www.wikiwand.com/en/Tidy_data

Tetromate_GoogleAssistantApplication

Google Assistant driven tetrode lowering. Let's you take notes about how tetrodes are being lowered with convenient voice commands. Works well with natural language e.g. "lower 5 on tetrode 6" or just "5 on 6", or even other variations. Automatically creates a webpage table representing your tetrode lowering notes.

CA1PFC_blender_models

3D brain models for pubs and presentations

data-pipeline

ryoung's current data processing pipeline in Jadhav Lab

DeepInsight

(ryoung mods) A general framework for interpreting wide-band neural activity

DI.jl

Julia based Data Interface for my electrophysiology and behavior data. All data types are Tidy Data based DataFrame objects (rows=samples, cols=properties of samples)

DIutils

This package split from a much larger git repo that comprised my julia lab code environment. Contains my homebrew utilties used on DI.jl based neural data analysis. Short one-off functions I lean on to save time often go here.

DynamicAxisWarping.jl

Dynamic Time Warping (DTW) and related algorithms in Julia, at Julia speeds

EnvironmentControlUnit-GoalFetchMaze

Code for our goal pursuit maze.

github2file

ry's fork of github2file :: modified for multi-file type and allowing local zip file input ... useful for passing githubrepo to gemini/claude/etc

GLM-CFC

A GLM based approach to measure CFC

GridSearch

Turn any script into a grid search. (ryoung's library)

julia-party-parrot

julia party parrot animation for funsies

julia-repl-vim

Julia REPL plugin for vim/neovim

NeuroMetrics.jl

Plots.jl

(ryoung mods) Powerful convenience for Julia visualizations and data analysis

RatInABox

(ryoung mods) A python package for modelling locomotion in complex environments and spatially/velocity selective cell activity.

replay_trajectory_classification

Identify whether replays are fragmented, continuous, or stationary.

Resume-Matcher

Resume Matcher is an open source, free tool to improve your resume. It works by using language models to compare and rank resumes with job descriptions.

SearchSortedNearest.jl

ryoung's modifications

seqNMF

ryoung's GPU modifications

SynapticSage