adamgayoso

nanodo

biology-for-ai

learning biology syllabus, geared for machine learning folks

matplotlib-label-lines

Label line using matplotlib.

kana

Single cell analysis in the browser

maxtext

A simple, performant and scalable Jax LLM!

PyComplexHeatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

typst-undergradmath

A Typst port of undergradmath

typst

A new markup-based typesetting system that is powerful and easy to learn.

cellarium-ml

Distributed single-cell data analysis.

veridical-flow

Making it easier to build stable, trustworthy data-science pipelines based on the PCS framework.

pml-book

"Probabilistic Machine Learning" - a book series by Kevin Murphy

redun

Yet another redundant workflow engine

lance

Modern columnar data format for ML and LLMs implemented in Rust. Convert from parquet in 2 lines of code for 100x faster random access, vector index, and data versioning. Compatible with Pandas, DuckDB, Polars, Pyarrow, with more integrations coming..

jaxtyping

Type annotations and runtime checking for shape and dtype of JAX/NumPy/PyTorch/etc. arrays. https://docs.kidger.site/jaxtyping/

hnswlib

Header-only C++/python library for fast approximate nearest neighbors

SnapATAC2

Single-cell epigenomics analysis tools

svglib

Read SVG files and convert them to other formats.

python-remote-pdb

Remote vanilla PDB (over TCP sockets).

scBasset-pytorch

An implementation of scBasset model in PyTorch.

tensordict

TensorDict is a pytorch dedicated tensor container.

pyslingshot

Python implementation of the Slingshot pseudotime algorithm

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

lutra

Ooops, I wrote another Sphinx theme! [very WIP, do not use]

reflex

🕸️ Web apps in pure Python 🐍

vanity

scRNA-Seq normalization for the vain

tfmodisco-lite

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.

glasbey

Algorithmically create or extend categorical colour palettes

jupyter-scatter

Interactive 2D scatter plot widget for Jupyter Lab and Notebook. Scales to millions of points!

BENGAL

Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets