jmschrei

best-of-ml-python

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

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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).

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

gReLU

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

logomaker

Software for the visualization of sequence-function relationships

skglm

Fast and modular sklearn replacement for generalized linear models

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

pygv

a minimal, scriptable genome browser for python

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.

ProCapNet

Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.

context-review

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