Python Biological-data-analysis Resources

muda A library for Musical Data Augmentation. muda package implements annotation-aware musical data augmentation, as described in the muda paper. The

Welcome to MARSYAS. MARSYAS is a software framework for rapid prototyping of audio applications, with flexibility and extensibility as primary concer

Essentia Essentia is an open-source C++ library for audio analysis and audio-based music information retrieval released under the Affero GPL license.

aubio aubio is a library to label music and sounds. It listens to audio signals and attempts to detect events. For instance, when a drum is hit, at wh

POT: Python Optimal Transport This open source Python library provide several solvers for optimization problems related to Optimal Transport for signa

emcee The Python ensemble sampling toolkit for affine-invariant MCMC emcee is a stable, well tested Python implementation of the affine-invariant ense

A supervised domain-agnostic framework that allows for probabilistic modelling, namely the prediction of probability distributions for individual data

Stable Baselines Stable Baselines is a set of improved implementations of reinforcement learning algorithms based on OpenAI Baselines. You can read a

Master status: Development status: Package information: scikit-rebate This package includes a scikit-learn-compatible Python implementation of ReBATE,

BoostARoota A Fast XGBoost Feature Selection Algorithm (plus other sklearn tree-based classifiers) Why Create Another Algorithm? Automated processes l

tsfresh This repository contains the TSFRESH python package. The abbreviation stands for "Time Series Feature extraction based on scalable hypothesis

"One of the holy grails of machine learning is to automate more and more of the feature engineering process." ― Pedro Domingos, A Few Useful Things to

dovpanda Directions OVer PANDAs Directions are hints and tips for using pandas in an analysis environment. dovpanda is an overlay companion for workin

Prodmodel is a build system for data science pipelines. Users, testers, contributors are welcome! Motivation · Concepts · Installation · Usage · Contr

meza: A Python toolkit for processing tabular data Index Introduction | Requirements | Motivation | Hello World | Usage | Interoperability | Installat

pyjanitor pyjanitor is a Python implementation of the R package janitor, and provides a clean API for cleaning data. Why janitor? Originally a port of

BatchFlow BatchFlow helps you conveniently work with random or sequential batches of your data and define data processing and machine learning workflo

pandas-ply: functional data manipulation for pandas pandas-ply is a thin layer which makes it easier to manipulate data with pandas. In particular, it

pdpipe ˨ Easy pipelines for pandas DataFrames (learn how!). Website: https://pdpipe.github.io/pdpipe/ Documentation: https://pdpipe.github.io/pdpipe/d

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

pandas API on Apache Spark Explore Koalas docs » Live notebook · Issues · Mailing list Help Thirsty Koalas Devastated by Recent Fires The Koalas proje

datatable This is a Python package for manipulating 2-dimensional tabular data structures (aka data frames). It is close in spirit to pandas or SFrame

Arctic TimeSeries and Tick store Arctic is a high performance datastore for numeric data. It supports Pandas, numpy arrays and pickled objects out-of-

pysparkling Pysparkling provides a faster, more responsive way to develop programs for PySpark. It enables code intended for Spark applications to exe

XPandas (extended Pandas) implements 1D and 2D data containers for storing type-heterogeneous tabular data of any type, and encapsulates feature extra

pandas-gbq pandas-gbq is a package providing an interface to the Google BigQuery API from pandas Installation Install latest release version via conda

Blaze translates a subset of modified NumPy and Pandas-like syntax to databases and other computing systems. Blaze allows Python users a familiar inte

Pandas Profiling Documentation | Slack | Stack Overflow Generates profile reports from a pandas DataFrame. The pandas df.describe() function is great

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

AI Explainability 360 (v0.2.1) The AI Explainability 360 toolkit is an open-source library that supports interpretability and explainability of datase

TensorFlow Model Analysis TensorFlow Model Analysis (TFMA) is a library for evaluating TensorFlow models. It allows users to evaluate their models on

ELI5 ELI5 is a Python package which helps to debug machine learning classifiers and explain their predictions. It provides support for the following m

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

Documentation | External Resources | Research Paper Shapley is a Python library for evaluating binary classifiers in a machine learning ensemble. The

HoloViews Stop plotting your data - annotate your data and let it visualize itself. HoloViews is an open-source Python library designed to make data a

fuck-coding-interviews This repository is created by an awkward programmer who always struggles with coding problems on LeetCode, even with some Easy

Algorithms and Data Structures (ands) Introduction This project was created for personal use mostly while studying for an exam (starting in the month

Algorithms in Python Implementations of a few algorithms and datastructures for fun and profit! Completed Karatsuba Multiplication Basic Sorting Rabin

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

keras-contrib : Keras community contributions Keras-contrib is deprecated. Use TensorFlow Addons. The future of Keras-contrib: We're migrating to tens

Reproduce, Automate, Scale your data science. Welcome to Polyaxon, a platform for building, training, and monitoring large scale deep learning applica

Here is Poutyne. Poutyne is a simplified framework for PyTorch and handles much of the boilerplating code needed to train neural networks. Use Poutyne

torchtext This repository consists of: torchtext.datasets: The raw text iterators for common NLP datasets torchtext.data: Some basic NLP building bloc

Website | Documentation | Tutorials | Installation | Release Notes CatBoost is a machine learning method based on gradient boosting over decision tree

Light Gradient Boosting Machine LightGBM is a gradient boosting framework that uses tree based learning algorithms. It is designed to be distributed a

ND DIAL: Imbalanced Algorithms Minimalist Python-based implementations of algorithms for imbalanced learning. Includes deep and representational learn

imbalanced-learn imbalanced-learn is a python package offering a number of re-sampling techniques commonly used in datasets showing strong between-cla

MLBox is a powerful Automated Machine Learning python library. It provides the following features: Fast reading and distributed data preprocessing/cle

Master status: Development status: Package information: TPOT stands for Tree-based Pipeline Optimization Tool. Consider TPOT your Data Science Assista

Time series analysis today is an important cornerstone of quantitative science in many disciplines, including natural and life sciences as well as eco

Prophet: Automatic Forecasting Procedure Prophet is a procedure for forecasting time series data based on an additive model where non-linear trends ar

tslearn The machine learning toolkit for time series analysis in Python Section Description Installation Installing the dependencies and tslearn Getti

pyGAM Generalized Additive Models in Python. Documentation Official pyGAM Documentation: Read the Docs Building interpretable models with Generalized

[Due to the time taken @ uni, work + hell breaking loose in my life, since things have calmed down a bit, will continue commiting!!!] [By the way, I'm

Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks. Sebastian Raschka 2014-2021 Links Doc

dlib C++ library Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real worl

What is xLearn? xLearn is a high performance, easy-to-use, and scalable machine learning package that contains linear model (LR), factorization machin

ark_invest daily weekday report of @arkinvest ETF activity + data collection This script was created to: Extract and save daily csv's from ARKInvest's

Lidar-data-decode In this project, you can decode your lidar data frame(pcap file) and make your own datasets(test dataset) in Windows without any hug

Introduction Yield explorer is a WIP! I needed a tool that would show me historical data and performance of my staked crypto but was unable to find a

Deep Illuminator Deep Illuminator is a data augmentation tool designed for image relighting. It can be used to easily and efficiently genera

Ultra-Data-Efficient GAN Training: Drawing A Lottery Ticket First, Then Training It Toughly Code for this paper Ultra-Data-Efficient GAN Tra

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

Table of contents What is PEM? Overview Installation Usage Executable Library Telegram Bot Try OPEM in Your Browser! MATLAB Issues & Bug Reports Contr

MOSAIC: A modular single-molecule analysis interface MOSAIC is a single molecule analysis toolbox that automatically decodes multi-state nanopore data

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

The latest information about Galaxy can be found on the Galaxy Community Hub. Community support is available at Galaxy Help. Galaxy Quickstart Galaxy

CKAN: The Open Source Data Portal Software CKAN is the world’s leading open-source data portal platform. CKAN makes it easy to publish, share and work

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

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure

A Python library that helps data scientists to infer causation rather than observing correlation.

Collaborate This is a web application for managing and building stories based on tips solicited from the public. This project is meant to be easy to s

Website • Docs • Blog • Twitter • Chat (Community & Support) • Tutorial • Mailing List Data Version Control or DVC is an open-source tool for data sci

Collaborate This is a web application for managing and building stories based on tips solicited from the public. This project is meant to be easy to s

Friture Friture is an application to visualize and analyze live audio data in real-time. Friture displays audio data in several widgets, such as a sco

Introduction Apiestas is a project composed of a backend powered by the awesome framework FastAPI and a crawler powered by Scrapy. This project has fo

This open source project serves two purposes. Collection and evaluation of a Question Answering dataset to improve existing QA/search methods - COVID-

MazeRL is an application oriented Deep Reinforcement Learning (RL) framework, addressing real-world decision problems. Our vision is to cover the complete development life cycle of RL applications ranging from simulation engineering up to agent development, training and deployment.

Easy to setup customizable honeypots for monitoring network traffic, bots activities and username\password credentials. The current available honeypot

Data Visualizer for Super Mario Kart (SNES)

Medical-Transformer Pytorch Code for the paper "Medical Transformer: Gated Axial-Attention for Medical Image Segmentation" About this repo: This repo

Algo-Phantom-Backend 💻 Algo-Phantoms-Backend is an Application that provides pathways and quizzes along with a code editor to help you towards your D

Photonix Photo Manager This is a photo management application based on web technologies. Run it on your home server and it will let you find what you

ocropy OCRopus is a collection of document analysis programs, not a turn-key OCR system. In order to apply it to your documents, you may need to do so

Boltons boltons should be builtins. Boltons is a set of over 230 BSD-licensed, pure-Python utilities in the same spirit as — and yet conspicuously mis

a BTC Clipper or a "Bitcoin Clipper" is a type of malware designed to target cryptocurrency transactions.

A PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf 2021). Abstract In this work we propose Pathfind

BaseSpec is a system that performs a comparative analysis of baseband implementation and the specifications of cellular networks. The key intuition of BaseSpec is that a message decoder in baseband software embeds the protocol specification in a machine-friendly structure to parse incoming messages;

SeaLion is designed to teach today's aspiring ml-engineers the popular machine learning concepts of today in a way that gives both intuition and ways of application. We do this through concise algorithms that do the job in the least jargon possible and examples to guide you through every step of the way.

Official code to reproduce the results and data presented in the paper Contrastive Learning Inverts the Data Generating Process.

xgbse: XGBoost Survival Embeddings "There are two cultures in the use of statistical modeling to reach conclusions from data

CANalyse is a tool built to analyze the log files to find out unique datasets automatically and able to connect to simple user interfaces suc

ForecastGA is a tool that combines a couple of popular libraries, Atspy and googleanalytics, with a few enhancements.

A package to aggregate gridded data in xarray to polygons in geopandas using area-weighting from the relative area overlaps between pixels and polygons. Check out the binder link above for a sample code run!

OpenClubhouse-Worker This is a simple worker for OpenClubhouse to sync CH channel data.

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.

Summarization, translation, Q&A, text generation and more at blazing speed using a T5 version implemented in ONNX. This package is still in alpha stag

gensim – Topic Modelling in Python Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora. Targ

WHAT: Supervised text vectorization tool Textvec is a text vectorization tool, with the aim to implement all the "classic" text vectorization NLP meth