Jason Chin

Peregrine. Peregrine: Fast Genome Assembler Using SHIMMER Index

ipython_d3_mashup. JavaScript

DCNet. DCNet — Denoising (DNA) Sequence With a LSTM-RNN and PyTorch & Neural DBG

peregrine-2021. Rust

Write_A_Genome_Assembler_With_IPython. The repository keeps the files for an IPython notebook on about how to make a simple genome assembler using python

pgr-tk. PGR-TK: Pangenome Research Tool Kit

wavefront-aln. A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring

CNP-clustering. Explore using "Conditional Neural Process" for clustering longitudinal data efficiently

multi-tabix. multi_tbx: a simple tool for indexing VCF files and extract variant records for variant data stored in multiple VCF files.

dash13-KIR-MHC-assemblies. Repository for code and small data set for Dash13 Hackathon

tron. Rust

kipoi_model_zoo_dx. example to run Deep Learning model to predict DNA sequence features with Kipoi with DNAnexus platform

MATER. MATER - Minimizer RNAseq HLA typer

DeepDiveDeepVariant. This repository is for hosting Jupyter notebooks for examining a couple of internal processes in DeepVariant

Falcon_the_very_original. Falcon: a set of small tools for fast aligning long reads for consensus and assembly

DALIGNER. Find all significant local alignments between reads

ai-gent-smith. "AI-Gent Smith" is a simple project demonstrating the use of Rust and various LLM libraries to build a web-based LLM agent library for users.

starview_app. a quick exercise using three-d library (https://github.com/asny/three-d) visualizing a 3D Spaticial Transcriptom data taset

algebra. A Boolean Algebra for Genetic Variants

Peregrine_dev. Python

mimalloc_rust. A Rust wrapper over Microsoft's MiMalloc memory allocator

petgraph. Graph data structure library for Rust.

rust-genai. Rust multiprovider generative AI client (Ollama, OpenAi, Anthropic, Groq, Gemini, Cohere, ...)

ipython. Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

agc. Assembled Genomes Compressor

VariantNET. A simple neural network for calling het-/hom-variants from alignments of single molecule reads to a reference

pgr-tk_archived. Rust