GitHub
https://github.com/kull-centre/prism
Software development pipelines related to the PRISM project
https://github.com/kull-centre/_2024_larsen-ledet_mlh1
data and scripts for "Disentangling the mutational effects on protein stability and interaction of human MLH1"
https://github.com/kull-centre/_2023_theisen_molecular_switching
Data files related to "Molecular switching in transcription through splicing and proline-isomerization regulates stress responses in plants" by Theisen et al. 2023
https://github.com/kull-centre/_2022_groenbaek-thygesen_aspa_mave
Scripts and data for Grønbæk-Thygesen et al
https://github.com/kull-centre/_2022_norrild_gmma_trx
Increasing protein stability by inferring substitution effects from high-throughput experiments
https://github.com/kumawatb/lifefromscratch
An implementation of Tim Hutton's Squirm3 artificial chemistry in Rust
https://github.com/kumiori/variational-jumps
Theoretical and numerical study of jump transitions in constrained variational evolution problems.
https://github.com/kumiori/indiscrete
How do elementary systems evolve, under irreversibility constraints?
https://github.com/kunalshah03/rufus
Rufus - Intelligent Web Scraper for RAG Systems
https://github.com/kunalshah03/darknet
YOLOv4 / Scaled-YOLOv4 / YOLO - Neural Networks for Object Detection (Windows and Linux version of Darknet )
https://github.com/kundajelab/procapnet
Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
https://github.com/kundajelab/immuneclip
CLIP-based model for aligning epitopes to immune receptors
https://github.com/kundajelab/fastism
In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.
https://github.com/kundajelab/retina-design
Designing AAV sequences for retinal cell types (with scATAC-seq models)
https://github.com/kundajelab/apricot
apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly.
https://github.com/kundajelab/alzheimers_parkinsons
Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis
https://github.com/kundajelab/1kg_ld_utils
utils/notes for LD calculation from 1000 genomes panel
https://github.com/kunpai/acadhashiru
The Expert Orchestrator AI: Dynamically Adapting, Budget-Aware, and Precisely Tailored to Your Needs
https://github.com/kundajelab/pybigwig
A python extension for quick access to bigWig files
https://github.com/kundajelab/neural_motif_discovery
Framework for interrogating transcription-factor motifs and their syntax/grammars from neural-network interpretations
https://github.com/kundajelab/chromdragonn
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
https://github.com/kundajelab/3dchromatin_replicateqc
Software to compute reproducibility and quality scores for Hi-C data
https://github.com/kundajelab/coessentiality
Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)
https://github.com/kundajelab/synapse-backup-syncer
Create and sync backups to Synapse
https://github.com/kundajelab/pylearn2
A Machine Learning library based on Theano
https://github.com/kunpai/llm-inference-cpp
Script to run LLM inference using C++
https://github.com/kunpai/ecs272-final-project
Final project for ECS272 class - InfoVis
https://github.com/kurokida/jspsych
A JavaScript library for creating and running behavioral experiments in a web browser
https://github.com/kunpengren/zclaim
Cross-chain private transactions between Zcash chains
https://github.com/kunpengren/sui-networks
A local multiple validator nodes sui network with fauce service
https://github.com/kunpengren/slimchain
Source code for the VLDB21 paper "SlimChain: Scaling Blockchain Transactions through Off-Chain Storage and Parallel Processing"
https://github.com/kunpengren/ethlocal
Build a local private Ethereum Network by docker container
https://github.com/kunzaatko/boundarylayerproblem
Resources and Beamer presentation for a talk about perturbation methods that leads to solving a non-linear differential equation with a boundary layer.
https://github.com/kunzaatko/promptingtools.jl
Streamline your life using PromptingTools.jl, the Julia package that simplifies interacting with large language models.