pssmgen • Rank 8.5 • Science 77%

Generates consistent PSSM and/or PDB files for protein-protein complexes

geofiles • Rank 8.5 • Science 77%

Evaluation of file formats in the context of geo-referenced 3D geometries.

nengo • Rank 18.5 • Science 67%

A Python library for creating and simulating large-scale brain models

Spectra • Rank 8.5 • Science 77%

Spectra.jl aims at helping treatment of spectral (Raman, Infrared, XAS, NMR) data under the Julia language

astrocalc • Rank 8.5 • Science 77%

An astronomer's calculator used to perform common calculations, conversions and measurements.

msdm • Rank 8.5 • Science 77%

Models of Sequential Decision-Making

earthaccess • Rank 21.5 • Science 64%

Python Library for NASA Earthdata APIs

smrnaseq • Rank 8.5 • Science 77%

A small-RNA sequencing analysis pipeline

SIAMFANLEquations • Rank 8.5 • Science 77%

This is a Julia package of nonlinear solvers. These codes are used in my book, Solving Nonlinear Equations with Iterative Methods: Solvers and Examples in Julia.

torchxrayvision • Rank 18.5 • Science 67%

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

tsfresh • Rank 26.4 • Science 59%

Automatic extraction of relevant features from time series:

metanno • Rank 8.4 • Science 77%

Annotator building tool for Jupyter

diffractsim • Rank 8.4 • Science 77%

✨🔬 A flexible diffraction simulator for exploring and visualizing physical optics.

biobb-model • Rank 8.4 • Science 77%

Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.

chipseq • Rank 8.4 • Science 77%

ChIP-seq peak-calling, QC and differential analysis pipeline.

dfa_identify • Rank 8.4 • Science 77%

Python library for identifying/learning DFAs from labeled examples by reduction to SAT.

dcm2bids • Rank 8.4 • Science 77%

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

openbenches.org • Rank 8.4 • Science 77%

OpenBenches.org - an open data repository for memorial benches

viralrecon • Rank 8.4 • Science 77%

Assembly and intrahost/low-frequency variant calling for viral samples

UnfoldMakie • Rank 8.4 • Science 77%

Plotting and visualization tools for EEG data, with additional Unfold.jl regression ERP methods. Based on the visualization libraries Makie.jl and AlgebraOfGraphics.jl

lmfitxps • Rank 8.4 • Science 77%

Models for fitting XPS-data with lmfit. Extends the Built-In Models of lmfit with a focus on XPS. Implements a Convolution of Gaussian/Doniach-Sunjic for signal fitting and various models for fitting the background in XPS, such as Tougaard, Shirley and Slope-background.

interpret • Rank 26.4 • Science 59%

Fit interpretable models. Explain blackbox machine learning.

Singularity Registry — Peer-reviewed • Rank 8.4 • Science 77%

Singularity Registry: Open Source Registry for Singularity Images - Published in JOSS (2017)

mmaction2 • Rank 21.3 • Science 64%

OpenMMLab's Next Generation Video Understanding Toolbox and Benchmark

uniplate • Rank 18.3 • Science 67%

Haskell library for simple, concise and fast generic operations.

pydicom • Rank 26.3 • Science 59%

Read, modify and write DICOM files with python code

kani • Rank 8.3 • Science 77%

kani (カニ) is a highly hackable microframework for tool-calling language models. (NLP-OSS @ EMNLP 2023)

algebra • Rank 31.3 • Science 54%

Libraries for finite field, elliptic curve, and polynomial arithmetic

sb3-contrib • Rank 21.3 • Science 64%

Contrib package for Stable-Baselines3 - Experimental reinforcement learning (RL) code

GRChombo — Peer-reviewed • Rank 8.3 • Science 77%

GRChombo: An adaptable numerical relativity code for fundamental physics - Published in JOSS (2021)

biobb-chemistry • Rank 8.3 • Science 77%

Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.

hist • Rank 21.3 • Science 64%

Histogramming for analysis powered by boost-histogram

KiteModels • Rank 8.3 • Science 77%

Kite and tether models for the simulation of kite power systems

cf-xarray • Rank 21.2 • Science 64%

an accessor for xarray objects that interprets CF attributes

dash • Rank 31.2 • Science 54%

Data Apps & Dashboards for Python. No JavaScript Required.

torchrl • Rank 26.2 • Science 59%

A modular, primitive-first, python-first PyTorch library for Reinforcement Learning.

hydragnn • Rank 10.2 • Science 75%

Distributed PyTorch implementation of multi-headed graph convolutional neural networks

somef • Rank 8.2 • Science 77%

SOftware Metadata Extraction Framework: A tool for automatically extracting relevant software information from readme files

datazimmer • Rank 10.2 • Science 75%

Data artifact orchestrator

opendal • Rank 31.2 • Science 54%

Apache OpenDAL: One Layer, All Storage.

core • Rank 10.2 • Science 75%

parallel finite element unstructured meshes

gstools • Rank 18.2 • Science 67%

GSTools - A geostatistical toolbox: random fields, variogram estimation, covariance models, kriging and much more

p-winds • Rank 8.2 • Science 77%

Python implementation of Parker wind models for exoplanet atmospheres

networkdynamics.jl • Rank 8.2 • Science 77%

Julia package for simulating Dynamics on Networks

flamegpu2 • Rank 8.2 • Science 77%

FLAME GPU 2 is a GPU accelerated agent based modelling framework for CUDA C++ and Python

thermopot • Rank 8.2 • Science 77%

Python package for calculating thermodynamic potentials from first-principles calculations

pydata-wrangler • Rank 8.2 • Science 77%

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

voodoonet • Rank 8.2 • Science 77%

Machine learning application for detecting liquid droplets in mixed-phase clouds using Doppler cloud radar spectra

hls-foundation-os • Rank 8.2 • Science 77%

This repository contains examples of fine-tuning Harmonized Landsat and Sentinel-2 (HLS) Prithvi foundation model.

drizzle • Rank 18.2 • Science 67%

A package for combining dithered images into a single image

avogadro • Rank 18.2 • Science 67%

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

pyalex • Rank 18.1 • Science 67%

A Python library for OpenAlex (openalex.org)

dnaio • Rank 18.1 • Science 67%

Efficiently read and write sequencing data from Python

python-intermediate-development • Rank 8.1 • Science 77%

"Intermediate Research Software Development Skills (Python)" Lesson Material

pysecs • Rank 8.1 • Science 77%

An open source library for calculating Spherical Elementary Current Systems (SECS)

biobb-structure-utils • Rank 8.1 • Science 77%

Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues.

tiatoolbox • Rank 18.1 • Science 67%

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

clarabel • Rank 23.1 • Science 62%

Clarabel.rs: Interior-point solver for convex conic optimisation problems in Rust.

ammico • Rank 10.1 • Science 75%

AI-based Media and Misinformation Content Analysis Tool: Analyze text and images

tmp-transformers • Rank 8.1 • Science 77%

biocommons.seqrepo • Rank 18.1 • Science 67%

non-redundant, compressed, journalled, file-based storage for biological sequences

biobb-io • Rank 8.1 • Science 77%

Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.

ofiber • Rank 8.0 • Science 77%

A python module for mode calculations in cylindrical and planar fibers.

itk-wasm • Rank 21.0 • Science 64%

High performance spatial analysis in a web browser and across programming languages and hardware architectures

mvsim • Rank 8.0 • Science 77%

Vehicle and mobile robotics simulator. C++ & Python API. Use it as a standalone application or via ROS 1 or ROS 2

spezillm • Rank 8.0 • Science 77%

Large Language Model (LLM) module for the Spezi Ecosystem

citation • Rank 8.0 • Science 77%

R package | create cff citation file from R package metadata

hydrogenerate • Rank 10.0 • Science 75%

Tool to estimate the hydropower potential of a site.

lat-epig • Rank 8.0 • Science 77%

The Lat-Epig interface allows you to query the EDCS and save the search result in a TSV file and plot the results on a map of the Roman Empire without any prior knowledge of programming.

bigtools • Rank 18.0 • Science 67%

A high-performance BigWig and BigBed library in Rust

JOSS Project 2 • Rank 0.0 • Science 85%

Scientific research

JOSS Project 1 • Rank 0.0 • Science 85%

Scientific research

JOSS Project 3 • Rank 0.0 • Science 85%

Scientific research

iasi • Rank 0.0 • Science 85%

This repository provides a collection of codes for the analysis of remote sensing observations of EUMETSAT's Infrared Atmospheric Sounding Interferometer (IASI).

gps • Rank 0.0 • Science 85%

This repository provides a collection of codes for the analysis of GPS/RO observations.

lwtnn • Rank 8.0 • Science 77%

light NN client

pymatviz • Rank 8.0 • Science 77%

A toolkit for visualizations in materials informatics.

best-of-atomistic-machine-learning • Rank 8.0 • Science 77%

🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.

openrefine-ecology-lesson • Rank 8.0 • Science 77%

Data Cleaning with OpenRefine for Ecologists

py3-semver • Rank 31.0 • Science 54%

Python package to work with Semantic Versioning (https://semver.org/)

gdal2 • Rank 7.9 • Science 77%

smart-transformers • Rank 7.9 • Science 77%

Smart Transformers are a versatile machine learning tool that can be integrated with Pytorch, TensorFlow, and JAX. Smart transformers provide accurate computations required for cryptographic algorithms. These transformers is that they are independent modules, making it efficient to experiment with various research projects related to cryptanalysis

jointly • Rank 7.9 • Science 77%

Jointly: A Python package for synchronizing sensors with accelerometer data

JetReconstruction • Rank 7.9 • Science 77%

Jet reconstruction (reclustering) with Julia

pye3sm • Rank 7.9 • Science 77%

PyE3SM: a Python library to assist E3SM model simulation.

lamem • Rank 7.9 • Science 77%

LaMEM (Lithosphere and Mantle Evolution Model) - a 3D parallel code to simulate geodynamic and geomechanical processes

simplification • Rank 17.9 • Science 67%

Very fast Python line simplification using either the RDP or Visvalingam-Whyatt algorithm implemented in Rust

muon • Rank 17.9 • Science 67%

muon is a multimodal omics Python framework

smac • Rank 20.9 • Science 64%

SMAC3: A Versatile Bayesian Optimization Package for Hyperparameter Optimization

spreadsheet-ecology-lesson • Rank 7.9 • Science 77%

Data Organization in Spreadsheets for Ecologists

ionmob • Rank 7.8 • Science 77%

An open-source prediction framework for peptide ion collision cross section (CCS) values with python.

Sundials • Rank 17.8 • Science 67%

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 • Rank 17.8 • Science 67%

Parameterizing neural power spectra into periodic & aperiodic components.

rowan • Rank 17.8 • Science 67%

A Python package for working with quaternions.

matsciml • Rank 7.8 • Science 77%

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 • Rank 17.8 • Science 67%

A tool to estimate time varying instantaneous reproduction number during epidemics

Diversity • Rank 7.8 • Science 77%

Julia package for diversity measurement

mdla • Rank 7.8 • Science 77%

Multivariate Dictionary Learning Algorithm

Zygote • Rank 20.8 • Science 64%

21st century AD

crosstl • Rank 7.8 • Science 77%

Universal Programming Language & Translator