GitHub
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/airscripts/kuma
A simple Docker Compose implementation of famous Uptime Kuma.
https://github.com/ait-assistive-autonomous-systems/3d_nonrigid_tricubic_pointcloud_registration
Non-rigid ICP-like point cloud registration algorithm using piece-wise tricubic polynomials as transformation model.
https://github.com/dmentipl/cocktails
Cocktails collected by Daniel Mentiplay (@dmentipl)
nakedape
♪♫sell heart. suitable for all ages. not always suitable for all creeds. essentially by definition. arses' cracked though. https://www.youtube.com/watch?v=NjvwWiCYLl4
https://github.com/dmentipl/super-earths-in-twhya
Super-Earths in the TW Hya disc
simulated-selfhood-llms
Code and data for the behavioral evaluation of introspective coherence in LLMs.
https://github.com/aliceo2group/aliceo2
O2 software project for the ALICE experiment at CERN
https://github.com/alleninstitute/mies
Multichannel Igor Electrophysiology Suite
https://github.com/dmentipl/multigrain
A smoothed particle hydrodynamics algorithm for multigrain dust with separate sets of particles
dreq_tools
Tools for updating the EERIE data request as well as the tables in various formats
https://github.com/dmentipl/flyby-observational-signatures
Flybys in protoplanetary discs - II. Observational signatures
sixarm_debian_zeromq_packages
SixArm.com » Debian » ZeroMQ packages for message queues
aims-dscbi
Data science course for Rwanda national statistical system (NSS) staff
https://github.com/amlalejini/alife-2025-env-conn
Holds supplemental materials, code, configuration settings, et cetera for 2025 ALife conference paper, "Environmental connectivity influences long-term evolutionary outcomes"
mitos_scripts.jl
Command Line Scripts for the MIToS Package to Analyze Protein Sequence and Structure
https://github.com/andim/pyrepseq
Python library for immune repertoire analysis
https://github.com/ankitbarik/topo_nutation
Code and figures for paper on nutation and dissipation due to topography at the core mantle boundary
https://github.com/annarufas/rufas_etal_2024_grl
Code and data necessary to reproduce the figures in our study "Can we Constrain Geographical Variability in the Biological Carbon Pump's Transfer Efficiency from Observations?".
https://github.com/ansleybrown1337/lysimeter-analysis
Python package that processes and analyzes weighing lysimeter data for quantifying crop water use (i.e., evapotranspiration).
