Python Protein-visualization Resources

Integrated Gradients This is the pytorch implementation of "Axiomatic Attribution for Deep Networks". The original tensorflow version could be found h

About DRIFT is a tool for Diachronic Analysis of Scientific Literature. The application offers user-friendly and customizable utilities for two modes:

Invariant Point Attention - Pytorch Implementation of Invariant Point Attention as a standalone module, which was used in the structure module of Alph

A Python library for reading, writing and visualizing the OMEGA Format, targeted towards storing reference and perception data in the automotive context on an object list basis with a focus on an urban use case.

Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverages the spatial coordinates of the data, as well as tissue images if available.

All-in-one web-based development environment for machine learning Getting Started • Features & Screenshots • Support • Report a Bug • FAQ • Known Issu

ProGen - (wip) Implementation and replication of ProGen, Language Modeling for Protein Generation, in Pytorch and Jax (the weights will be made easily

streamlit-tensorboard This is a work-in-progress, providing a function to embed TensorBoard, TensorFlow's visualization toolkit, in Streamlit apps. In

Temporal network visualization This code is what I used to make the visualizations of SocioPatterns' primary school data here It requires the data of

JittorVis - Visual understanding of deep learning model.

RLCard Showdown This is the GUI support for the RLCard project and DouZero project. RLCard-Showdown provides evaluation and visualization tools to hel

kaggle-hpa-2021-7th-place-solution Code for 7th place solution of Human Protein Atlas - Single Cell Classification on Kaggle. A description of the met

HUMAP Hierarchical Manifold Approximation and Projection (HUMAP) is a technique based on UMAP for hierarchical non-linear dimensionality reduction. HU

Denoising Diffusion Probabilistic Model for Proteins Implementation of Denoising Diffusion Probabilistic Model in Pytorch. It is a new approach to gen

Statistics and Visualization of acceptance rate, main keyword of CVPR 2021 accepted papers for the main Computer Vision conference (CVPR)

LinkedIn Connections Analyzer 🔗 https://linkedin-analzyer.herokuapp.com Hey hey 👋 , welcome to my LinkedIn connections analyzer. I recently found ou

streamlit-letsplot This is a work-in-progress, providing a convenience function to plot charts from the Lets-Plot visualization library. Example usage

[TensorFlow] Protein Interface Prediction using Graph Convolutional Networks Unofficial TensorFlow implementation of Protein Interface Prediction usin

Blockchain ✨ Learn Blockchains by Building One Yourself Installation Make sure Python 3.6+ is installed. Install Flask Web Framework. Clone this repos

ProteinLM We pretrain protein language model based on Megatron-LM framework, and then evaluate the pretrained model results on TAPE (Tasks Assessing P

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

Visualizing Adapted Knowledge in Domain Transfer @inproceedings{hou2021visualizing, title={Visualizing Adapted Knowledge in Domain Transfer}, auth

Plot, scatter plots and histograms in the terminal using braille dots, with (almost) no dependancies. Plot with color or make complex figures - similar to a very small sibling to matplotlib. Or use the canvas to plot dots and lines yourself.

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

ProteinBERT is a universal protein language model pretrained on ~106M proteins from the UniRef90 dataset. Through its Python API, the pretrained model can be fine-tuned on any protein-related task in a matter of minutes. Based on our experiments with a wide range of benchmarks, ProteinBERT usually achieves state-of-the-art performance. ProteinBERT is built on TenforFlow/Keras.

DeepFRI Deep functional residue identification Citing @article {Gligorijevic2019, author = {Gligorijevic, Vladimir and Renfrew, P. Douglas and Koscio

Graph-Based Protein Design This repo contains code for Generative Models for Graph-Based Protein Design by John Ingraham, Vikas Garg, Regina Barzilay

Structural basis for solubility in protein expression systems Large-scale protein production for biotechnology and biopharmaceutical applications rely

notebookJS enables the execution of custom JavaScript code in Python Notebooks (Jupyter Notebook and Google Colab). This Python library can be useful for implementing and reusing interactive Data Visualizations in the Notebook environment.

DexYCB Toolkit DexYCB Toolkit is a Python package that provides evaluation and visualization tools for the DexYCB dataset. The dataset and results wer

Sequence-to-sequence framework with a focus on Neural Machine Translation based on Apache MXNet

SummVis is an interactive visualization tool for analyzing abstractive summarization model outputs and datasets.

Visualization Toolbox for Long Short Term Memory networks (LSTMs)

sankee Visualize changes in classified time series data with interactive Sankey plots in Google Earth Engine Contents Description Installation Using P

FlashTorch A Python visualization toolkit, built with PyTorch, for neural networks in PyTorch. Neural networks are often described as "black box". The

D3D Devkit for 3D: Some utils for 3D object detection and tracking based on Numpy and Pytorch Please consider siting my work if you find this library

This is a highly practical and example-based guide on visually representing data in reports and dashboards.

ipyleaflet A Jupyter / Leaflet bridge enabling interactive maps in the Jupyter notebook. Usage Selecting a basemap for a leaflet map: Loading a geojso

geoplot: geospatial data visualization geoplot is a high-level Python geospatial plotting library. It's an extension to cartopy and matplotlib which m

felicette Satellite imagery for dummies. What can you do with this tool? TL;DR: Generate JPEG earth imagery from coordinates/location name with public

OSMnx OSMnx is a Python package that lets you download geospatial data from OpenStreetMap and model, project, visualize, and analyze real-world street

Automatic neural network visualizations generated in your browser!

Tool for visualizing attention in the Transformer model (BERT, GPT-2, Albert, XLNet, RoBERTa, CTRL, etc.)

Apache Superset is a Data Visualization and Data Exploration Platform

emb-ntua-workshop This workshop discusses introductory concepts of machine learning and data mining following a hands-on approach using popular tools

NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

PyTorch Implementation of Generic Attention-model Explainability for Interpreting Bi-Modal and Encoder-Decoder Transformers 1 Using Colab Please notic

Geographic visualizations for HoloViews. Build Status Coverage Latest dev release Latest release Docs What is it? GeoViews is a Python library that ma

ipyleaflet A Jupyter / Leaflet bridge enabling interactive maps in the Jupyter notebook. Usage Selecting a basemap for a leaflet map: Loading a geojso

deck.gl | Website WebGL2-powered, highly performant large-scale data visualization deck.gl is designed to simplify high-performance, WebGL-based visua

Visual Automata Copyright 2021 Lewi Lie Uberg Released under the MIT license Visual Automata is a Python 3 library built as a wrapper for Caleb Evans'

git-cola: The highly caffeinated Git GUI git-cola is a powerful Git GUI with a slick and intuitive user interface. Copyright (C) 2007-2020, David Agu

yacv: Yet Another Compiler Visualizer yacv is a tool for visualizing various aspects of typical LL(1) and LR parsers. Check out demo on YouTube to see

MMdnn MMdnn is a comprehensive and cross-framework tool to convert, visualize and diagnose deep learning (DL) models. The "MM" stands for model manage

What is Vaex? Vaex is a high performance Python library for lazy Out-of-Core DataFrames (similar to Pandas), to visualize and explore big tabular data

Logging MXNet Data for Visualization in TensorBoard Overview MXBoard provides a set of APIs for logging MXNet data for visualization in TensorBoard. T

tensorboardX Write TensorBoard events with simple function call. The current release (v2.1) is tested on anaconda3, with PyTorch 1.5.1 / torchvision 0

Lucid Lucid is a collection of infrastructure and tools for research in neural network interpretability. We're not currently supporting tensorflow 2!

CapsNet-Visualization For more information on capsule networks check out my Medium articles here and here. Setup Use pip to install the required pytho

Welcome to Scikit-plot Single line functions for detailed visualizations The quickest and easiest way to go from analysis... ...to this. Scikit-plot i

Yellowbrick Visual analysis and diagnostic tools to facilitate machine learning model selection. What is Yellowbrick? Yellowbrick is a suite of visual

physt P(i/y)thon h(i/y)stograms. Inspired (and based on) numpy.histogram, but designed for humans(TM) on steroids(TM). The goal is to unify different

Chartify Chartify is a Python library that makes it easy for data scientists to create charts. Why use Chartify? Consistent input data format: Spend l

Hera Train/evaluate a Keras model, get metrics streamed to a dashboard in your browser. Setting up Step 1. Plant the spy Install the package pip

Orange Data Mining Orange is a data mining and visualization toolbox for novice and expert alike. To explore data with Orange, one requires no program

Mayavi: 3D visualization of scientific data in Python Mayavi docs: http://docs.enthought.com/mayavi/mayavi/ TVTK docs: http://docs.enthought.com/mayav

an interactive explorer for single-cell transcriptomics data cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell tra

Differentiable molecular simulation of proteins with a coarse-grained potential This repository contains the learned potential, simulation scripts and

The HyperNetX library provides classes and methods for the analysis and visualization of complex network data. HyperNetX uses data structures designed to represent set systems containing nested data and/or multi-way relationships. The library generalizes traditional graph metrics to hypergraphs.

Sockeye This package contains the Sockeye project, an open-source sequence-to-sequence framework for Neural Machine Translation based on Apache MXNet

Text preprocessing, representation and visualization from zero to hero. From zero to hero • Installation • Getting Started • Examples • API • FAQ • Co

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

ivis Implementation of the ivis algorithm as described in the paper Structure-preserving visualisation of high dimensional single-cell datasets. Ivis

PyWaffle PyWaffle is an open source, MIT-licensed Python package for plotting waffle charts. It provides a Figure constructor class Waffle, which coul

AutoViz Automatically Visualize any dataset, any size with a single line of code. AutoViz performs automatic visualization of any dataset with one lin

animatplot A python package for making interactive as well as animated plots with matplotlib. Requires Python = 3.5 Matplotlib = 2.2 (because slider

Lets-Plot Lets-Plot is an open-source plotting library for statistical data. It is implemented using the Kotlin programming language. The design of Le

In-depth EDA (target analysis, comparison, feature analysis, correlation) in two lines of code! Sweetviz is an open-source Python library that generat

JoyPy JoyPy is a one-function Python package based on matplotlib + pandas with a single purpose: drawing joyplots (a.k.a. ridgeline plots). The code f

openTSNE openTSNE is a modular Python implementation of t-Distributed Stochasitc Neighbor Embedding (t-SNE) [1], a popular dimensionality-reduction al

Introduction The facets project contains two visualizations for understanding and analyzing machine learning datasets: Facets Overview and Facets Dive

Chartify Chartify is a Python library that makes it easy for data scientists to create charts. Why use Chartify? Consistent input data format: Spend l

"To deal with hyper-planes in a 14 dimensional space, visualize a 3D space and say 'fourteen' very loudly. Everyone does it." - Geoff Hinton Overview

PyVista Deployment Build Status Metrics Citation License Community 3D plotting and mesh analysis through a streamlined interface for the Visualization

Perspective is an interactive visualization component for large, real-time datasets. Originally developed for J.P. Morgan's trading business, Perspect

missingno Messy datasets? Missing values? missingno provides a small toolset of flexible and easy-to-use missing data visualizations and utilities tha

VisPy: interactive scientific visualization in Python Main website: http://vispy.org VisPy is a high-performance interactive 2D/3D data visualization

PyQtGraph A pure-Python graphics library for PyQt5/PyQt6/PySide2/PySide6 Copyright 2020 Luke Campagnola, University of North Carolina at Chapel Hill h

UMAP Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, bu

Altair http://altair-viz.github.io Altair is a declarative statistical visualization library for Python. With Altair, you can spend more time understa

Bokeh is an interactive visualization library for modern web browsers. It provides elegant, concise construction of versatile graphics, and affords hi

Dash Dash is the most downloaded, trusted Python framework for building ML & data science web apps. Built on top of Plotly.js, React and Flask, Dash t

seaborn: statistical data visualization Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing

plotly.py Latest Release User forum PyPI Downloads License Data Science Workspaces Our recommended IDE for Plotly’s Python graphing library is Dash En

Sockeye This package contains the Sockeye project, an open-source sequence-to-sequence framework for Neural Machine Translation based on Apache MXNet

Text preprocessing, representation and visualization from zero to hero. From zero to hero • Installation • Getting Started • Examples • API • FAQ • Co

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

ivis Implementation of the ivis algorithm as described in the paper Structure-preserving visualisation of high dimensional single-cell datasets. Ivis

PyWaffle PyWaffle is an open source, MIT-licensed Python package for plotting waffle charts. It provides a Figure constructor class Waffle, which coul

AutoViz Automatically Visualize any dataset, any size with a single line of code. AutoViz performs automatic visualization of any dataset with one lin