PyCM — Peer-reviewed • Rank 22.3 • Science 98%

PyCM: Multiclass confusion matrix library in Python - Published in JOSS (2018)

Missingno — Peer-reviewed • Rank 24.2 • Science 93%

Missingno: a missing data visualization suite - Published in JOSS (2018)

corner.py — Peer-reviewed • Rank 21.8 • Science 95%

corner.py: Scatterplot matrices in Python - Published in JOSS (2016)

Visions — Peer-reviewed • Rank 22.2 • Science 93%

Visions: An Open-Source Library for Semantic Data - Published in JOSS (2020)

Stingray 2 — Peer-reviewed • Rank 17.1 • Science 95%

Stingray 2: A fast and modern Python library for spectral timing - Published in JOSS (2024)

FSharpGephiStreamer — Peer-reviewed • Rank 13.3 • Science 98%

FSharpGephiStreamer: An idiomatic bridge between F# and network visualization - Published in JOSS (2019)

piecewise-regression (aka segmented regression) in Python — Peer-reviewed • Rank 17.7 • Science 93%

piecewise-regression (aka segmented regression) in Python - Published in JOSS (2021)

uravu — Peer-reviewed • Rank 10.4 • Science 100%

uravu: Making Bayesian modelling easy(er) - Published in JOSS (2020)

Astronomical échelle spectroscopy data analysis with `muler` — Peer-reviewed • Rank 12.1 • Science 98%

Astronomical échelle spectroscopy data analysis with `muler` - Published in JOSS (2022)

THzTools — Peer-reviewed • Rank 9.5 • Science 100%

THzTools: data analysis software for terahertz time-domain spectroscopy - Published in JOSS (2024)

Cellpy – an open-source library for processing and analysis of battery testing data — Peer-reviewed • Rank 16.3 • Science 93%

Cellpy – an open-source library for processing and analysis of battery testing data - Published in JOSS (2024)

PyVBMC — Peer-reviewed • Rank 11.1 • Science 98%

PyVBMC: Efficient Bayesian inference in Python - Published in JOSS (2023)

TransBigData — Peer-reviewed • Rank 15.7 • Science 93%

TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization - Published in JOSS (2022)

ChainoPy — Peer-reviewed • Rank 8.9 • Science 98%

ChainoPy: A Python Library for Discrete Time Markov Chain Based Stochastic Analysis - Published in JOSS (2024)

PII-Codex — Peer-reviewed • Rank 8.6 • Science 98%

PII-Codex: a Python library for PII detection, categorization, and severity assessment - Published in JOSS (2023)

PyUnfold — Peer-reviewed • Rank 10.7 • Science 95%

PyUnfold: A Python package for iterative unfolding - Published in JOSS (2018)

spiketools — Peer-reviewed • Rank 5.0 • Science 100%

spiketools: a Python package for analyzing single-unit neural activity - Published in JOSS (2023)

PiSCAT — Peer-reviewed • Rank 9.9 • Science 95%

PiSCAT: A Python Package for Interferometric Scattering Microscopy - Published in JOSS (2022)

PIVA: Photoemission Interface for Visualization and Analysis • Rank 9.5 • Science 95%

PIVA: Photoemission Interface for Visualization and Analysis - Published in JOSS (2025)

scikit-learn • Rank 40.3 • Science 64%

scikit-learn: machine learning in Python

PatchView — Peer-reviewed • Rank 9.0 • Science 95%

PatchView: A Python Package for Patch-clamp Data Analysis and Visualization - Published in JOSS (2022)

Hypothesize — Peer-reviewed • Rank 11.0 • Science 93%

Hypothesize: Robust Statistics for Python - Published in JOSS (2020)

HiPart — Peer-reviewed • Rank 10.8 • Science 93%

HiPart: Hierarchical Divisive Clustering Toolbox - Published in JOSS (2023)

nimCSO — Peer-reviewed • Rank 5.0 • Science 98%

nimCSO: A Nim package for Compositional Space Optimization - Published in JOSS (2024)

ronswanson — Peer-reviewed • Rank 6.1 • Science 95%

ronswanson: Building Table Models for 3ML - Published in JOSS (2023)

visxhclust — Peer-reviewed • Rank 8.0 • Science 93%

visxhclust: An R Shiny package for visual exploration of hierarchical clustering - Published in JOSS (2022)

pypillometry — Peer-reviewed • Rank 7.9 • Science 93%

pypillometry: A Python package for pupillometric analyses - Published in JOSS (2020)

h3ppy — Peer-reviewed • Rank 7.1 • Science 93%

h3ppy: An open-source Python package for modelling and fitting H$_3^+$ spectra - Published in JOSS (2025)

ctbench - compile-time benchmarking and analysis — Peer-reviewed • Rank 4.9 • Science 95%

ctbench - compile-time benchmarking and analysis - Published in JOSS (2023)

pandas • Rank 40.8 • Science 59%

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

latentcor — Peer-reviewed • Rank 4.4 • Science 95%

latentcor: An R Package for estimating latent correlations from mixed data types - Published in JOSS (2021)

ConTEXT Explorer — Peer-reviewed • Rank 4.4 • Science 95%

ConTEXT Explorer: a web-based text analysis tool for exploring and visualizing concepts across time - Published in JOSS (2021)

tbeptools — Peer-reviewed • Rank 4.4 • Science 95%

tbeptools: An R package for synthesizing estuarine data for environmental research - Published in JOSS (2021)

pypots • Rank 21.6 • Science 77%

A Python toolkit/library for reality-centric machine/deep learning and data mining on partially-observed time series, including SOTA neural network models for scientific analysis tasks of imputation/classification/clustering/forecasting/anomaly detection/cleaning on incomplete industrial (irregularly-sampled) multivariate TS with NaN missing values

plotastic — Peer-reviewed • Rank 5.3 • Science 93%

plotastic: Bridging Plotting and Statistics in Python - Published in JOSS (2024)

StatAid — Peer-reviewed • Rank 2.6 • Science 95%

StatAid: An R package with a graphical user interface for data analysis - Published in JOSS (2020)

A MATLAB toolbox to detect and analyze marine heatwaves — Peer-reviewed • Rank 4.2 • Science 93%

A MATLAB toolbox to detect and analyze marine heatwaves - Published in JOSS (2019)

scikit-mobility • Rank 18.4 • Science 77%

scikit-mobility: mobility analysis in Python

kangas • Rank 15.9 • Science 77%

🦘 Explore multimedia datasets at scale

plotnine • Rank 28.7 • Science 64%

A Grammar of Graphics for Python

awkward • Rank 14.6 • Science 77%

Manipulate JSON-like data with NumPy-like idioms.

xarrayutils • Rank 13.8 • Science 77%

statsmodels • Rank 35.5 • Science 54%

Statsmodels: statistical modeling and econometrics in Python

pygwalker • Rank 24.6 • Science 64%

PyGWalker: Turn your dataframe into an interactive UI for visual analysis

iris • Rank 11.5 • Science 77%

A powerful, format-agnostic, and community-driven Python package for analysing and visualising Earth science data

pyerrors • Rank 11.3 • Science 77%

Error propagation and statistical analysis for Monte Carlo simulations in lattice QCD and statistical mechanics using autograd.

decode • Rank 12.5 • Science 75%

:zap: DESHIMA code for data analysis

mudata • Rank 18.6 • Science 67%

Multimodal Data (.h5mu) implementation for Python

pydata-wrangler • Rank 8.2 • Science 77%

Wrangle messy numerical, image, and text data into consistent well-organized formats

collapse • Rank 20.3 • Science 64%

Advanced and Fast Data Transformation in R

chip-atlas • Rank 6.2 • Science 77%

ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser

cf-python • Rank 15.7 • Science 67%

A CF-compliant Earth Science data analysis library

spectrochempy • Rank 14.0 • Science 67%

SpectroChemPy is a framework for processing, analyzing and modeling spectroscopic data for chemistry with Python

gradio • Rank 34.4 • Science 46%

Build and share delightful machine learning apps, all in Python. 🌟 Star to support our work!

hsds • Rank 16.1 • Science 64%

Cloud-native, service based access to HDF data

dimensio • Rank 2.4 • Science 77%

Multivariate Data Analysis - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/dimensio

deerlab • Rank 11.9 • Science 67%

Python package for data analysis for dipolar EPR spectroscopy

https://github.com/alan-turing-institute/clevercsv • Rank 21.7 • Science 57%

CleverCSV is a Python package for handling messy CSV files. It provides a drop-in replacement for the builtin CSV module with improved dialect detection, and comes with a handy command line application for working with CSV files.

pandas-ai • Rank 24.5 • Science 54%

Chat with your database or your datalake (SQL, CSV, parquet). PandasAI makes data analysis conversational using LLMs and RAG.

DIVAnd • Rank 11.0 • Science 67%

DIVAnd performs an n-dimensional variational analysis of arbitrarily located observations

gemdat • Rank 10.1 • Science 67%

Python toolkit for molecular dynamics analysis

pygmmis • Rank 10.0 • Science 67%

Gaussian mixture model for incomplete (missing or truncated) and noisy data

gsppy • Rank 9.8 • Science 67%

GSP (Generalized Sequence Pattern) algorithm in Python

aspecd • Rank 9.6 • Science 67%

Python framework for handling spectroscopic data focussing on reproducibility

suite2p • Rank 17.1 • Science 59%

cell detection in calcium imaging recordings

https://github.com/zblz/naima • Rank 15.8 • Science 59%

Derivation of non-thermal particle distributions through MCMC spectral fitting

deepgraph • Rank 15.0 • Science 59%

Analyze Data with Pandas-based Networks. Documentation:

fmflow • Rank 6.9 • Science 67%

:zap: Data analysis package for FMLO

cloupy • Rank 6.7 • Science 67%

CLOUPY IS NO LONGER SUPPORTED. PLEASE, SEE README. cloupy is a Python library for climatological data downloading, processing and visualizing. The main goal of the library is to help its author in writing a BA thesis. The library is well adapted to academic work - used data sources are reliable and graphs are easy to modify.

pyglotaran • Rank 14.7 • Science 59%

A Python library for Global and Target Analysis of time-resolved spectroscopy data

cwepr • Rank 6.5 • Science 67%

A Python package based on the ASpecD framework for handling cwEPR data.

pyprobables • Rank 18.6 • Science 54%

Probabilistic data structures in python http://pyprobables.readthedocs.io/en/latest/index.html

obscure_stats • Rank 5.1 • Science 67%

A small collection of lesser-known statistical measures

interactive_data_editor • Rank 4.6 • Science 67%

A Software to interactively edit data in a graphical manner

de.lmu.ifi.dbs.elki • Rank 17.1 • Science 54%

ELKI Data Mining Toolkit

corems • Rank 11.5 • Science 59%

CoreMS is a comprehensive mass spectrometry software framework

conexp-clj • Rank 14.8 • Science 54%

A General-Purpose Tool for Formal Concept Analysis

streamlit • Rank 32.7 • Science 36%

Streamlit — A faster way to build and share data apps.

public_open_source_data_science • Rank 1.1 • Science 67%

A repository of open source data science projects for social good

hyperspy • Rank 21.1 • Science 46%

Multidimensional data analysis

nfstream • Rank 18.1 • Science 49%

NFStream: a Flexible Network Data Analysis Framework.

imbalanced-learn • Rank 30.6 • Science 36%

A Python Package to Tackle the Curse of Imbalanced Datasets in Machine Learning

https://github.com/modelscope/data-juicer • Rank 19.2 • Science 46%

Data processing for and with foundation models! 🍎 🍋 🌽 ➡️ ➡️🍸 🍹 🍷

ydata-profiling • Rank 28.7 • Science 36%

1 Line of code data quality profiling & exploratory data analysis for Pandas and Spark DataFrames.

https://github.com/airbytehq/airbyte • Rank 28.6 • Science 36%

The leading data integration platform for ETL / ELT data pipelines from APIs, databases & files to data warehouses, data lakes & data lakehouses. Both self-hosted and Cloud-hosted.

https://github.com/uxlfoundation/scikit-learn-intelex • Rank 28.1 • Science 36%

Extension for Scikit-learn is a seamless way to speed up your Scikit-learn application

https://github.com/lancedb/lance • Rank 28.1 • Science 36%

Modern columnar data format for ML and LLMs implemented in Rust. Convert from parquet in 2 lines of code for 100x faster random access, vector index, and data versioning. Compatible with Pandas, DuckDB, Polars, Pyarrow, and PyTorch with more integrations coming..

https://github.com/growthbook/growthbook • Rank 28.1 • Science 36%

Open Source Feature Flagging and A/B Testing Platform

kneed • Rank 9.3 • Science 54%

Knee point detection in Python :chart_with_upwards_trend:

https://github.com/flyteorg/flyte • Rank 27.3 • Science 36%

Scalable and flexible workflow orchestration platform that seamlessly unifies data, ML and analytics stacks.

https://github.com/rapidsai/cudf • Rank 26.6 • Science 36%

cuDF - GPU DataFrame Library

qpcr • Rank 8.5 • Science 54%

A python package to analyse qPCR data for single-use or high-throughput application

https://github.com/elementary-data/elementary • Rank 26.2 • Science 36%

The dbt-native data observability solution for data & analytics engineers. Monitor your data pipelines in minutes. Available as self-hosted or cloud service with premium features.

mastercurves • Rank 8.2 • Science 54%

Python package for automatically superimposing data sets to create a master curve, using Gaussian process regression and maximum a posteriori estimation.

popmon • Rank 17.7 • Science 44%

Monitor the stability of a Pandas or Spark dataframe ⚙︎

https://github.com/alleninstitute/openscope_databook • Rank 7.5 • Science 54%

OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈

datawranglingpy • Rank 4.4 • Science 57%

Minimalist Data Wrangling with Python (Open-Access Textbook)

epiphyte • Rank 7.0 • Science 54%

Python toolkit for working with high-dimensional neural data recorded during naturalistic, continuous stimuli @a-darcher @rachrapp

https://github.com/root-project/root • Rank 14.6 • Science 46%

The official repository for ROOT: analyzing, storing and visualizing big data, scientifically

classix • Rank 10.6 • Science 49%

Fast and explainable clustering in Python