GitHub
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"
stats-strided-wasm-dmeanwd
Calculate the arithmetic mean of a double-precision floating-point strided array using Welford's algorithm.
installkernel-wsl
Script and installkernel hook to copy Linux kernel to the host system and update .wslconfig.
fair-convergence-matrix
Basic code to create FAIR convergence matrix from nanodash nanopublications
sequencecomposition
Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition
neuco-bench
Welcome to NeuCo-Bench, a benchmarking framework for evaluating compressed embeddings on downstream tasks.
pmv-si-2023-2-pe1-t2-house-hero
pmv-si-2023-2-pe1-t2-house-hero created by GitHub Classroom
https://github.com/ivorytower152/denoising-diffusion-pytorch
Implementation of Denoising Diffusion Probabilistic Model in Pytorch
eista
A single-cell spatial transcriptomics pipeline aimed at covering all analysis stages from quantification and clustering to tertiary analyses.
lkfmixer
LKFMixer: Exploring Large Kernel Feature For Efficient Image Super-Resolution
https://github.com/boyle-lab/gpatch-manuscript
Data retrieval and Analysis steps for the GPatch manuscript.
presentation.template
This repository contains latex templates for NumPEx documents
neuropyxels
NeuroPyxels (npyx) is a python library built for electrophysiologists using Neuropixels electrodes. This package stems from the need of a pythonist who really did not want to transition to MATLAB to work with Neuropixels: it features a suite of core utility functions for loading, processing and plotting Neuropixels data.
ssp-mmc
A Stochastic Shortest Path Algorithm for Optimizing Spaced Repetition Scheduling
recoll
Recoll is a desktop full-text search tool (forked from the original at framagit)
https://github.com/ivorytower152/mmpose
OpenMMLab Pose Estimation Toolbox and Benchmark.
aises-virtue-ethics
Teach virtue ethics to AI, an alternative approach to ConstitutionalAI. Final project for the AISES course, fall 2025
repilot
Repilot, a patch generation tool introduced in the ESEC/FSE'23 paper "Copiloting the Copilots: Fusing Large Language Models with Completion Engines for Automated Program Repair"
hermes_metadata_lesson
Data and Metadata in the Humanities: Structures, Schemas, and Standards
pyigmap
[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences
libs.tn
Automatische data extractie en dataverwerking voor de TN studie aan de HHS
bioc-rnaseq
Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
hermes_stat_inf_data_vis
Statistical inference and data visualization for the humanities
la-rape-ia
Markov 2000 est une râpe à fromage modifié pour "rapper des mots" grâce au modèle de Markov.
judy
Judy is a python library and framework to evaluate the text-generation capabilities of Large Language Models (LLM) using a Judge LLM.
elphbolt
A solver for the coupled and decoupled electron and phonon Boltzmann transport equations.
def-au-asls-soil-prof
Machine-readable representation of the classifiers described in chapter 8 Soil Profile, by R.C. McDonald and R.F. Isbell, in Australian soil and land survey field handbook (3rd edn)
https://github.com/dcan-labs/abcd-func
A citizen science game for ABCD Study Quality Control of functional image registration.
stripepy-hic
StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning
mlscalib
A ML python-based package implementing a variety of the state-of-the-art ML-based SCA techniques that is easy to use and easy to extend.
scanometrics
Python package for automated normative modeling of MRI anatomical scans
open-medical-r1
This repository is aim to reproduce the R1-Zero on medical domain.
