GitHub
ionmob
An open-source prediction framework for peptide ion collision cross section (CCS) values with python.
Sundials
Julia interface to Sundials, including a nonlinear solver (KINSOL), ODE's (CVODE and ARKODE), and DAE's (IDA) in a SciML scientific machine learning enabled manner
fooof
Parameterizing neural power spectra into periodic & aperiodic components.
matsciml
Open MatSci ML Toolkit is a framework for prototyping and scaling out deep learning models for materials discovery supporting widely used materials science datasets, and built on top of PyTorch Lightning, the Deep Graph Library, and PyTorch Geometric.
EpiEstim
A tool to estimate time varying instantaneous reproduction number during epidemics
pycopancore
reference implementation of the copan:CORE World-Earth modelling framework
rf-detr
RF-DETR is a real-time object detection model architecture developed by Roboflow, SOTA on COCO and designed for fine-tuning.
pyquarc
The pyQuARC tool reads and evaluates metadata records with a focus on the consistency and robustness of the metadata. pyQuARC flags opportunities to improve or add to contextual metadata information in order to help the user connect to relevant data products. pyQuARC also ensures that information common to both the data product and the file-level metadata are consistent and compatible. pyQuARC frees up human evaluators to make more sophisticated assessments such as whether an abstract accurately describes the data and provides the correct contextual information. The base pyQuARC package assesses descriptive metadata used to catalog Earth observation data products and files. As open source software, pyQuARC can be adapted and customized by data providers to allow for quality checks that evolve with their needs, including checking metadata not covered in base package.
CrystalNets
A julia package for the manipulation of crystal net representations and topology
pypsa-fes
A model that optimises investment and operation, and incorporates flexibility domestic demand flexibility to model scenarios for Great Britain's future energy system.
octotiger
Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees
biorad
R package for analysis and visualisation of biological signals in weather radar data
https://github.com/bluebrain/tmd
A python package for the topological analysis of neurons.
lizard
A simple code complexity analyser without caring about the C/C++ header files or Java imports, supports most of the popular languages.
OpenSkill
OpenSkill: A faster asymmetric multi-team, multiplayer rating system - Published in JOSS (2024)
rsmine
A Python package for efficient optimisation of real-space renormalization group transformations using Tensorflow.
Express
Express: a high-level, extensible workflow framework for accelerating ab initio calculations for the materials science community
transposonmapper
This repository contains the code for the transposonmapper package to map the transposons from the SATAY sequencing data.
adapt-diagnostics
A package for designing activity-informed nucleic acid diagnostics for viruses.
cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
chromatic_tda
Tool to compute six-packs of persistence diagrams for chromatic point clouds [packaged on PyPI]
optivorbis
🗜️ Library and application for lossless, format-preserving, two-pass optimization and repair of Vorbis data, reducing its size without altering any audio information.
worcs
Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)
ekpmeasure
Repository of analysis and computer control code for various experiments. Analysis module is designed to help the researcher wrangle large amounts of meta data
phaser
Phaser is a fun, free and fast 2D game framework for making HTML5 games for desktop and mobile web browsers, supporting Canvas and WebGL rendering.
macpan2
Tools for building and calibrating compartmental models of infectious disease.
oumi
Easily fine-tune, evaluate and deploy gpt-oss, Qwen3, DeepSeek-R1, or any open source LLM / VLM!
Container Tree
Container Tree: Software to Model Container Filesystems, Packages, and Inheritance - Published in JOSS (2019)
pydlr
Library for discrete Lehmann representation of imaginary time Green's functions
collapse
Advanced and Fast Data Transformation in R
pythonnumericaldemos
Well-documented Python demonstrations for spatial data analytics, geostatistical and machine learning to support my courses.
imagezmq
A set of Python classes that transport OpenCV images from one computer to another using PyZMQ messaging.
best-of-ps
🏆 A weekly updated ranked list of popular open-source libraries and tools for Power System Analysis.
articledownloader
Uses publisher APIs to programmatically retrieve scientific journal articles for text mining.
pycortex
Pycortex is a python-based toolkit for surface visualization of fMRI data
rockfinder
A python package and command-line suite to generate solar-system body ephemerides and to determine if specific transient detections are in fact known asteroids
ModelingToolkit
An acausal modeling framework for automatically parallelized scientific machine learning (SciML) in Julia. A computer algebra system for integrated symbolics for physics-informed machine learning and automated transformations of differential equations
irl-imitation
Implementation of Inverse Reinforcement Learning (IRL) algorithms in Python/Tensorflow. Deep MaxEnt, MaxEnt, LPIRL
magnets
A Python package to aggregate and reduce water distribution network models
OUTRIDER
OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
mmtrack
OpenMMLab Video Perception Toolbox. It supports Video Object Detection (VID), Multiple Object Tracking (MOT), Single Object Tracking (SOT), Video Instance Segmentation (VIS) with a unified framework.
codecarbon
Track emissions from Compute and recommend ways to reduce their impact on the environment.
labelfusion
Implementation of various label fusion approaches for medical imaging.
open-grid-emissions
Tools for producing high-quality hourly generation and emissions data for U.S. electric grids
onglai-classify-homologues
OngLai: A cheminformatics algorithm to classify homologous chemical series
o2r-meta
Metadata toolsuite for an extract-map-validate workflow supporting reproducible research
khroma
Colour Schemes for Scientific Data Visualization - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/khroma
harmonica
Forward modeling, inversion, and processing gravity and magnetic data
sqlmodel
SQL databases in Python, designed for simplicity, compatibility, and robustness.
datastew
Python library for intelligent data stewardship using Large Language Model (LLM) embeddings
XGI
XGI: A Python package for higher-order interaction networks - Published in JOSS (2023)
trufflesqueak
A Squeak/Smalltalk VM and Polyglot Programming Environment for the GraalVM.
python-neo
Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats
novu
The open-source notification Inbox infrastructure. E-mail, SMS, Push and Slack Integrations.
https://github.com/theislab/cellrank
CellRank: dynamics from multi-view single-cell data
