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Starred repositories
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
A list of deep learning implementations in biology
SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platf…
Dependency-aware deep generative models for multitasking analysis of spatial genomics data
🚀 One-stop solution for creating your digital avatar from chat history 💡 Fine-tune LLMs with your chat logs to capture your unique style, then bind to a chatbot to bring your digital self to life. …
Source Code for FINCH Clustering Algorithm
3D geoms for plotnine (grammar of graphics in Python)
Small utilities for working with fastq sequence files.
Match up paired end fastq files quickly and efficiently.
persistent caching to memory, disk, or database
Tools to process and analyze deep sequencing data.
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…
Official git repository for Biopython (originally converted from CVS)
Pretraining infrastructure for multi-hybrid AI model architectures
Genome modeling and design across all domains of life
Parametric sweep of simulated microbial communities and metagenomic sequencing.
SGLang is a fast serving framework for large language models and vision language models.
Heroes of the Storm match tracker for personal statistics
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
Visualize and annotate genomic coverage with ggplot2
Lab Materials for MIT 6.S191: Introduction to Deep Learning