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best-of-ml-python

🏆 A ranked list of awesome machine learning Python libraries. Updated weekly.

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jittor

Jittor is a high-performance deep learning framework based on JIT compiling and meta-operators.

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

checklist

Beyond Accuracy: Behavioral Testing of NLP models with CheckList

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

setup-python

Set up your GitHub Actions workflow with a specific version of Python

palmerpenguins

A great intro dataset for data exploration & visualization (alternative to iris).

pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks

pyCirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

pyfaidx

Efficient pythonic random access to fasta subsequences

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

jupyter-scatter

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

chromap

Fast alignment and preprocessing of chromatin profiles

path_explain

A repository for explaining feature attributions and feature interactions in deep neural networks.

logomaker

Software for the visualization of sequence-function relationships

foldcomp

Compressing protein structures effectively with torsion angles

spectrum_utils

Python package for efficient mass spectrometry data processing and visualization

chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

scBasset

Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.

vak

A neural network framework for researchers studying acoustic communication

UWThesis

Class file for University of Washington thesis formatting with LaTeX.

ml-pitfalls

Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"

rtist

Color palettes from famous artists and paintings.

fastISM

In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.

minimal-viable-package

Demonstrate how to structure a project, build Python packages, unit testing, GitHub Actions, Read the Docs (RTD), package managers, distributions, containers, and high performance computing (HPC).

pomegranate-mathematica

Wolfram Mathematica distributions parser for pomegranate

peax-avocado

Avocado encoder model for Peax

apricot-benchmark