modelcif • Rank 14.9 • Science 67%

Python package for handling ModelCIF mmCIF and BinaryCIF files

SymbolicRegression • Rank 17.9 • Science 64%

Distributed High-Performance Symbolic Regression in Julia

posted • Rank 4.9 • Science 77%

POSTED: Potsdam open-source techno-economic database

brendapyrser • Rank 4.9 • Science 77%

A Python parser for the BRENDA database

ltc • Rank 4.9 • Science 77%

Latimer Core

sigprofilermatrixgenerator • Rank 14.9 • Science 67%

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

kableExtra • Rank 22.9 • Science 59%

Construct Complex Table with knitr::kable() + pipe.

genome-mining-workshop • Rank 4.9 • Science 77%

Genome Mining Workshop Overview

supar • Rank 14.9 • Science 67%

:rocket: State-of-the-art parsers for natural language.

goslin • Rank 4.9 • Science 77%

Goslin is the Grammar on succinct lipid nomenclature.

Ciclope — Peer-reviewed • Rank 4.9 • Science 77%

Ciclope: micro Computed Tomography to Finite Elements - Published in JOSS (2023)

iad • Rank 4.9 • Science 77%

Forward and Inverse Radiative Transport using the Adding-Doubling method

echopype • Rank 14.9 • Science 67%

Enabling interoperability and scalability in ocean sonar data analysis

xeofs — Peer-reviewed • Rank 14.9 • Science 67%

xeofs: Comprehensive EOF analysis in Python with xarray - Published in JOSS (2024)

omegaconf • Rank 27.8 • Science 54%

Flexible Python configuration system. The last one you will ever need.

mne-connectivity • Rank 17.8 • Science 64%

Connectivity algorithms that leverage the MNE-Python API.

pyrho • Rank 6.8 • Science 75%

A virtual optogenetics laboratory

pmidcite • Rank 4.8 • Science 77%

Download "Cited by" data from the NIH for any paper with a PubMed ID

datahugger • Rank 14.8 • Science 67%

One downloader for many scientific data and code repositories! DOI :open_hands: Data

promptsource • Rank 17.8 • Science 64%

Toolkit for creating, sharing and using natural language prompts.

virtualizarr • Rank 17.8 • Science 64%

Cloud-Optimize your Scientific Data as Virtual Zarr stores, using xarray syntax.

cameratrapai • Rank 14.8 • Science 67%

AI models trained by Google to classify species in images from motion-triggered wildlife cameras.

WaterWaves1D • Rank 4.8 • Science 77%

Water wave models in one dimension

speziviews • Rank 4.8 • Science 77%

A common set of SwiftUI views and related functionality used in Spezi modules

tsinfer • Rank 14.8 • Science 67%

Infer a tree sequence from genetic variation data.

https://github.com/fgnt/meeteval • Rank 14.8 • Science 67%

MeetEval - A meeting transcription evaluation toolkit

cellpose • Rank 22.8 • Science 59%

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

geograph • Rank 9.8 • Science 72%

GeoGraph provides a tool for analysing habitat fragmentation and related problems in landscape ecology. GeoGraph builds a geospatially referenced graph from land cover or field survey data and enables graph-based landscape ecology analysis as well as interactive visualizations.

relaxed • Rank 9.8 • Science 72%

Provides differentiable versions of common HEP operations and objectives.

clinker • Rank 14.8 • Science 67%

Gene cluster comparison figure generator

PhyloNetworks • Rank 14.7 • Science 67%

PhyloNetworks: a julia package with utilities for phylogenetic networks

excelnumericaldemos • Rank 4.7 • Science 77%

A set of numerical demonstrations in Excel to assist with teaching / learning concepts in probability, statistics, spatial data analytics and geostatistics. I hope these resources are helpful, Prof. Michael Pyrcz

manyecoevo • Rank 4.7 • Science 77%

Software for analysing Many-Analysts' style data and generating the ManyEcoEvo project data

eclipse-sumo • Rank 22.7 • Science 59%

Eclipse SUMO is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation.

ncnn • Rank 27.7 • Science 54%

ncnn is a high-performance neural network inference framework optimized for the mobile platform

fpa_lr • Rank 14.7 • Science 67%

Filter of Pairwise Alignement

skosprovider • Rank 14.7 • Science 67%

A python abstraction for SKOS vocabularies

pyloudnorm • Rank 22.6 • Science 59%

Flexible audio loudness meter in Python with implementation of ITU-R BS.1770-4 loudness algorithm

reacnetgenerator • Rank 14.6 • Science 67%

an automatic reaction network generator for reactive molecular dynamics simulation

fsrs4anki-optimizer • Rank 14.6 • Science 67%

A modern Anki custom scheduling based on Free Spaced Repetition Scheduler algorithm

geo-tide-backend • Rank 4.6 • Science 77%

Backend source code to produce geospatial data layers for the MCSC's Geospatial Trucking Industry Decarbonization Explorer (Geo-TIDE)

manim • Rank 27.6 • Science 54%

A community-maintained Python framework for creating mathematical animations.

rnadnavar • Rank 4.6 • Science 77%

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

shico • Rank 4.6 • Science 77%

Netherlands eScience Center - Shifting Concepts Through Time project

kvpress • Rank 14.6 • Science 67%

LLM KV cache compression made easy

geodatasets • Rank 4.6 • Science 77%

Synthetic datasets for geoscience (geo)statistical modeling

retomaton • Rank 9.6 • Science 72%

PyTorch code for the RetoMaton paper: "Neuro-Symbolic Language Modeling with Automaton-augmented Retrieval" (ICML 2022)

gribscan • Rank 4.6 • Science 77%

Create indices for GRIB files and provide an xarray interface.

hexwatershed • Rank 4.6 • Science 77%

The C++ backend of the HexWatershed a mesh independent flow direction model for hydrologic models

lambda-dti • Rank 4.6 • Science 77%

Interpreter of the ITGL with dynamic type inference

isoseq • Rank 4.6 • Science 77%

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

gcs_python • Rank 4.5 • Science 77%

Graduated cylindrical shell CME model in Python

pyvista-1 • Rank 4.5 • Science 77%

jsonschema • Rank 35.5 • Science 46%

An implementation of the JSON Schema specification for Python

mossco-code • Rank 4.5 • Science 77%

Backup of sf.net mossco/code git repository

micrometaapp-omero • Rank 4.5 • Science 77%

This is a limited-functionality, beta - implementation of the integration of Micro-Meta App in the OMERO.web client

pandoc • Rank 27.5 • Science 54%

Universal markup converter

SphereUDE • Rank 4.5 • Science 77%

A Julia package for regression in the sphere based on Universal Differential Equations

rnanorm • Rank 14.5 • Science 67%

Normalization of RNA-seq gene expression

pydriller • Rank 22.4 • Science 59%

Python Framework to analyse Git repositories

topas_tools • Rank 4.4 • Science 77%

Set of scripts for working with Topas

https://github.com/bluebrain/snap • Rank 14.4 • Science 67%

The Blue Brain Pythonic Simulation and Network Analysis Productivity layer

pygeoogc • Rank 14.4 • Science 67%

A part of HyRiver software stack for accessing ArcGIS RESTful-, WFS-, and WMS-based web services.

seismic-zfp • Rank 14.4 • Science 67%

Compress and decompress seismic data

mrpro • Rank 14.4 • Science 67%

MR image reconstruction and processing.

cdk • Rank 27.4 • Science 54%

The Chemistry Development Kit

hyperspectral-regression • Rank 4.4 • Science 77%

Code examples for the book chapter "Supervised, Semi-Supervised and Unsupervised Learning for Hyperspectral Regression".

skosprovider-getty • Rank 14.4 • Science 67%

Skosprovider implementation of the Getty Vocabularies

pythae • Rank 17.4 • Science 64%

Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

tpot • Rank 22.4 • Science 59%

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.

BisPy — Peer-reviewed • Rank 4.4 • Science 77%

BisPy: Bisimulation in Python - Published in JOSS (2021)

vegperiod • Rank 14.3 • Science 67%

R Package to determine Thermal Vegetation Periods

cytodataframe • Rank 4.3 • Science 77%

An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

mpds-client • Rank 4.3 • Science 77%

MPDS API client library in Python

armory-testbed • Rank 14.3 • Science 67%

ARMORY Adversarial Robustness Evaluation Test Bed

torchopt • Rank 17.3 • Science 64%

TorchOpt is an efficient library for differentiable optimization built upon PyTorch.

vedo • Rank 22.3 • Science 59%

A python module for scientific analysis of 3D data based on VTK and Numpy

cpprb • Rank 14.3 • Science 67%

Fast Flexible Replay Buffer Library (Mirror repository of https://gitlab.com/ymd_h/cpprb)

pypsa-eur-project • Rank 4.3 • Science 77%

xarray-dataclass • Rank 4.3 • Science 77%

:zap: xarray data creation by data classes

radiipolynomial.jl • Rank 4.3 • Science 77%

Library for computer-assisted proofs in dynamical systems

ebcpy • Rank 14.3 • Science 67%

pyrtools • Rank 14.3 • Science 67%

image pyramid code in python 3

https://github.com/bluebrain/efel • Rank 9.2 • Science 72%

Electrophys Feature Extraction Library

spec2vec • Rank 14.2 • Science 67%

Word2Vec based similarity measure of mass spectrometry data.

pyaudioanalysis • Rank 22.2 • Science 59%

Python Audio Analysis Library: Feature Extraction, Classification, Segmentation and Applications

nuflux • Rank 9.2 • Science 72%

A library for calculating atmospheric neutrino fluxes.

package-boutroslab-plotting-general • Rank 14.2 • Science 67%

Functions to Create Publication-Quality Plots

sinergym • Rank 14.2 • Science 67%

Gym environment for building simulation and control using reinforcement learning

biopython • Rank 32.2 • Science 49%

Official git repository for Biopython (originally converted from CVS)

maftools • Rank 22.2 • Science 59%

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

polarimetry • Rank 4.2 • Science 77%

Polarimetry for the decay Λc → p K π

spezicontact • Rank 4.2 • Science 77%

Spezi module to display contact information

multi-task-pybullet-drones • Rank 4.2 • Science 77%

laserfarm • Rank 14.2 • Science 67%

Laserchicken Framework for Applications in Research in Macro-ecology

DFTK • Rank 14.1 • Science 67%

Density-functional toolkit

ray • Rank 35.1 • Science 46%

Ray is an AI compute engine. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.

ecoconsprereg • Rank 4.1 • Science 77%

Designing, Evaluating and Testing Preregistration Templates for Ecology and Conservation

block2 • Rank 14.1 • Science 67%

Efficient parallel quantum chemistry DMRG in MPO formalism

torchtune • Rank 27.1 • Science 54%

PyTorch native post-training library