pickleton89

scToppR

An API wrapper for ToppGene

OligoFormer

functional_enrichment_analysis

A DIY guide to gene ontology, pathway, and gene set enrichment analysis

pygwalker

PyGWalker: Turn your pandas dataframe into an interactive UI for visual analysis

ai-research-assistant

Aria is Your AI Research Assistant Powered by GPT Large Language Models

notero-notes

A Zotero plugin for syncing items and notes into Notion

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

graphrag

A modular graph-based Retrieval-Augmented Generation (RAG) system

LLM101n

LLM101n: Let's build a Storyteller

MALAT1_threshold

lifelong-learning-system-template

This repository is a getting started kit for a lifelong learning system with Obsidian and Anki.

pandas_exercises

Practice your pandas skills!

Complete-Python-Bootcamp

GeneNMF

Methods to discover gene programs on single-cell data

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

Python_Data_Analytics_Course

My 'Python for Data Analytics' course on YouTube

aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.

HCNetlas

Human cell-type-specific network atlas (HCNetlas) and network-based single-cell RNA-seq data analysis

SeqLengthPlot

An easy-to-use Python-based Tool for Visualizing and Retrieving Sequence Lengths from fasta files with a Tunable Splitting Point

ai-fundamentals

Learn the fundamentals of building AI solutions using Python.

easy-local-rag

SuperEasy 100% Local RAG with Ollama + Email RAG

scientific-visualization-book

An open access book on scientific visualization using python and matplotlib

KRAGEN

Software to implement GoT with a weviate vectorized database

mergekit

Tools for merging pretrained large language models.

litgpt

20+ high-performance LLMs with recipes to pretrain, finetune and deploy at scale.

overlapping_assays

Code and datasets from the manuscript "Comparing IC50 or Ki values from different sources is a source of significant noise".

OncLLMExtraction

Expert-Curated Oncology Reports to Advance Language Model Inference

mulea

mulea - an R package for enrichment analysis using various ontologies and empirical false discovery rate

bonito

A lightweight library for generating synthetic instruction tuning datasets for your data without GPT.

Bioinformatics-with-Python-Cookbook-third-edition

Bioinformatics with Python Cookbook, Third Edition