maxibor

annotated_deep_learning_paper_implementations

🧑‍🏫 60 Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), gans(cyclegan, stylegan2, ...), 🎮 reinforcement learning (ppo, dqn), capsnet, distillation, ... 🧠

diffusers

🤗 Diffusers: State-of-the-art diffusion models for image and audio generation in PyTorch and FLAX.

pyscript

Try PyScript: https://pyscript.com Examples: https://tinyurl.com/pyscript-examples Community: https://discord.gg/HxvBtukrg2

memray

Memray is a memory profiler for Python

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

TabPFN

Official implementation of the TabPFN paper (https://arxiv.org/abs/2207.01848) and the tabpfn package.

firefox-translations

Firefox Translations is a webextension that enables client side translations for web browsers.

GPBoost

Combining tree-boosting with Gaussian process and mixed effects models

redun

Yet another redundant workflow engine

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

patchworklib

Patchwork for matplotlib: A subplot manager for intuitive layouts in matplotlib, seaborn, and plotnine.

pyCircos

python Circos

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

CheckM2

Assessing the quality of metagenome-derived genome bins using machine learning

nf-test

Simple test framework for Nextflow pipelines

parasail-python

Python bindings for the parasail C library.

pr2database

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

admix

an admixture analysis tool for Python that supports raw data from 23andme, AncestryDNA, etc.

pytaxonkit

Python bindings for the TaxonKit library

pykew

Python library for accessing Kew's data services

pathPhynder

A workflow for integrating ancient lineages into present-day phylogenies.

GGisy

Genome-Genome circle synteny

bacdive-api

iTOL

A Python API and a command-line tool for the Tree of Life

Wallen_DAMethodCompare_2021

Repository for data and code used in the manuscript "Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing"

admixfrog

decOM

🗑️🦷 decOM 🦷🗑️

TransforKmers

[WIP] A task-agnostic facility to pretrain/finetune/use a Transformer based model to classify your biological sequences.

PIAWeb

PIAWeb - a graphical web interface for PIA