https://github.com/bioconductor/bioconductor-training • Science 49%

Bioconductor teaching and education committee

https://github.com/biodataanalysisgroup/virtual-tutorial-perturbation-modelling • Science 49%

https://github.com/biodt/uc-grassland • Science 49%

pDT grassland main repository

https://github.com/bioinfomachinelearning/multicom4 • Science 49%

The MULTICOM4 protein structure prediction system developed by the Bioinformatics and Machine Learning Lab at the University of Missouri - Columbia

https://github.com/biolink/resource-ingest-guide-schema • Science 44%

A LinkML schema for describing the scope, rationale, and modeling approach for ingesting content from a single source.

https://github.com/biont-training/hpc-workflows-en • Science 44%

https://github.com/bioscan-ml/barcodebert • Science 49%

A pre-trained representation from a transformers model for inference on insect DNA barcoding data.

gcdm-sbdd • Science 54%

A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)

https://github.com/bodenmillergroup/imcdataanalysis • Science 49%

R based workflow for multiplexed imaging data

https://github.com/boothgroup/vayesta • Science 49%

A Python package for wave function-based quantum embedding

https://github.com/bootphon/speech-map • Science 49%

Mean Average Precision over words or n-grams with speech features

https://github.com/bozenne/article-netbenefit-correction • Science 49%

Code and software for the article "Correcting the bias of the net benefit estimator due to right-censored observations" published in biometrical (link: https://doi.org/10.1002/bimj.202000001 ).

csnet • Science 67%

https://github.com/brainets/hosi_infogain • Science 49%

Script for "Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning"

https://github.com/brainglobe/brainglobe-template-builder • Science 49%

Build unbiased anatomical templates from individual images

desirna • Science 67%

State of the art software for RNA sequence design. The first to solve the Eterna benchmark!

https://github.com/broadinstitute/profiling-resistance-mechanisms • Science 57%

Predicting pharmacodynamic responses to cancer drugs using cell morphology

https://github.com/broadinstitute/strainge • Science 57%

strain-level analysis tools

https://github.com/broadinstitute/pbs-analysis • Science 57%

Scripts for analyzing ChIP-seq and related datatypes with binning and PBS

https://github.com/broadinstitute/dino4cells_analysis • Science 57%

https://github.com/brugr9/uepluginvolumecreator • Science 49%

Unreal Engine Plugin: Volume Creator – Documentation

https://github.com/bueler/glacier-fe-estimate • Science 46%

extend the Falk technique to Stokes glacier models of surface evolution

https://github.com/cafferychen777/cafferychen777 • Science 49%

https://github.com/cair/tsetlinmachine • Science 49%

Code and datasets for the Tsetlin Machine

https://github.com/caltechlibrary/2020-05-11-swc-online • Science 52%

May 2020 Software Carpentry Workshop

https://github.com/camilogarciabotero/biovossencoder.jl • Science 46%

A small Julia package to represent BioSequences as a Voss matrix

https://github.com/catalystneuro/surmeier-lab-to-nwb • Science 49%

https://github.com/cbg-ethz/influenza_wastewater_analysis • Science 57%

https://github.com/cdcgov/dengue_epidemic_thresholds • Science 57%

https://github.com/cdcgov/irma • Science 57%

IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.

https://github.com/ceed/nekrs • Science 49%

Mirror of NekRS - GPU-oriented version of Nek5000. Please use the official repository, https://github.com/Nek5000/nekRS, to create issues and pull requests.

https://github.com/centre-for-humanities-computing/llm-tweet-classification • Science 49%

Classifying tweets with large language models with zero- and few-shot learning.

https://github.com/cgeoga/vecchia.jl • Science 49%

Vecchia approximations for Gaussian log-likelihoods

https://github.com/ch-earth/openfews • Science 49%

Open and Shareable Delft-FEWS configuration for connecting the Next Generation of Forecasting Tools

https://github.com/chakravala/staticvectors.jl • Science 44%

Statically sized tuple vectors for Julia

https://github.com/chenzhaiyu/ahninpainter • Science 49%

A toolset for AHN inpainting

https://github.com/choropent/3dseg • Science 49%

https://github.com/cidgoh/nf-ncov-voc • Science 49%

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.

https://github.com/climate-service-center/dacstore • Science 49%

Acceptance analysis DACStorE

https://github.com/climatecompatiblegrowth/geo-x-data-prep • Science 49%

Spatial data preparation tools for GeoH2 users.

https://github.com/clir-abvi-portal/clir-abvi-portal-aaslh • Science 44%

https://github.com/cmendl/rqcopt_hpc • Science 49%

HPC implementation of Riemannian quantum circuit optimization

https://github.com/coderefinery/testing • Science 57%

Automated testing - Preventing yourself and others from breaking your functioning code

https://github.com/coin-or/symphony • Science 49%

SYMPHONY is an open-source solver, callable library, and development framework for mixed-integer linear programs (MILPs) written in C with a number of unique features

https://github.com/comp-physics/meshfreetrixi.jl • Science 49%

Meshfree extension to Trixi using RBF-based numerics

https://github.com/compiler-campusminden/cpl-vorlesung-master-w25 • Science 44%

Lecture "Concepts of Programming Languages" (M.Sc.) (Winter 2025/26)

https://github.com/computational-biology-aachen/synechocystis-photosynthesis-2024 • Science 49%

A mathematical model of photosynthetic electron transport in Synechocystis sp. PCC 6803

https://github.com/conect2ai/sbai2025-tensorflores • Science 49%

https://github.com/corybrunson/ordr • Science 49%

manage ordinations and render biplots in a tidyverse workflow

https://github.com/cosbidev/ostransformer • Science 49%

Official implementation for the paper ``A Deep Learning Approach for Overall Survival Prediction in Lung Cancer with Missing Values´´

https://github.com/cosmo-pop/flowfusion • Science 54%

Generative modelling using diffusion models and flow-matching

https://github.com/cpanse/fgczqcms • Science 46%

https://github.com/crsu-apps/popviz • Science 49%

A visualisation package to show absolute effects as a proportion of people

https://github.com/csinva/clinical-rule-development • Science 49%

Building and vetting clinical decision rules.

https://github.com/cthoyt/wikidata-client • Science 54%

https://github.com/ctu-vras/monoforce • Science 49%

[IROS 2024] [ICML 2024 Workshop Differentiable Almost Everything] MonoForce: Learnable Image-conditioned Physics Engine

number-float64-base-assert-is-same-value-zero • Science 44%

Test if two double-precision floating-point numbers are the same value.

assignment1 • Science 44%

https://github.com/cwwhitney/urban_school_gardens • Science 49%

Decision model on investment in urban school gardens for food environment outcomes (Hanoi, Vietnam case)

https://github.com/cyclotronresearchcentre/bidsme_containerisation • Science 44%

Bringing BIDSme into a container, then NeuroDesk

https://github.com/danielathome19/engram-neural-network • Science 49%

tensorflow-engram: A Python package for Engram Neural Networks, adding biologically-inspired Hebbian memory and engram layers to TensorFlow/Keras models, supporting memory traces, plasticity, attention, and sparsity for neural sequence learning.

https://github.com/danielenricocahall/danielenricocahall • Science 49%

https://github.com/danielenricocahall/keras-unet • Science 49%

Implementation of U-Net in Keras

https://github.com/data-science-in-mechanical-engineering/mixed_precision_for_jax • Science 57%

A repository for Mixed Precision Training in JAX based on Equinox.

https://github.com/dataunitylab/jsonoid-discovery • Science 57%

Distributed JSON schema discovery

ads • Science 44%

Graphem - JAX: Node Influence Maximization via Geometric Embeddings • Science 98%

Graphem - JAX: Node Influence Maximization via Geometric Embeddings - Published in JOSS (2025)

Pi4Micronaut: A Java Library for IoT Research Instruments on Raspberry Pi • Science 93%

Pi4Micronaut: A Java Library for IoT Research Instruments on Raspberry Pi - Published in JOSS (2025)

REA_auth_review • Science 44%

Litstudy for performing mapping reviews

@stdlib/array-empty-like • Science 44%

Create an uninitialized array having the same length and data type as a provided array.

dh-youtube-database • Science 67%

Database for a YouTube centered Research for a Political Science PhD

amused • Science 54%

qsort R package — Peer-reviewed • Science 93%

qsort R package: A New Tool for Scoring Q-sort Data - Published in JOSS (2018)

complexity-in-complexity • Science 54%

Code for "Complexity in Complexity: Understanding Visual Complexity Through Structure, Color, and Surprise". CogSci, 2025 & ICLR Re-Align Workshop, 2025.

beamletoptics.jl • Science 67%

Optics simulation in Julia using geometrical and Gaussian beamlet tracing – simulate lasers, beam propagation, and simple optical systems.

OrbDot — Peer-reviewed • Science 93%

OrbDot: A Python package for studying the secular evolution of exoplanet orbits - Published in JOSS (2025)

activitywatch • Science 67%

The best free and open-source automated time tracker. Cross-platform, extensible, privacy-focused.

kcl-orss • Science 44%

materials for KCL Open Research Summer School

ginjax — Peer-reviewed • Science 93%

ginjax: E(d)-Equivariant CNN for Tensor Images - Published in JOSS (2025)

GraphCalc — Peer-reviewed • Science 93%

GraphCalc: A Python Package for Computing Graph Invariants in Automated Conjecturing Systems - Published in JOSS (2025)

scmorph — Peer-reviewed • Science 98%

scmorph: a Python package for analysing single-cell morphological profiles - Published in JOSS (2025)

slap2-utils — Peer-reviewed • Science 93%

slap2-utils: Tools for Processing SLAP2 Data - Published in JOSS (2025)

CaNS-Fizzy — Peer-reviewed • Science 93%

CaNS-Fizzy: A GPU-accelerated finite difference solver for turbulent two-phase flows - Published in JOSS (2025)

TMLE.jl — Peer-reviewed • Science 98%

TMLE.jl: Targeted Minimum Loss-Based Estimation in Julia - Published in JOSS (2025)

MCSimMod — Peer-reviewed • Science 93%

MCSimMod: An R Package for Working with Ordinary Differential Equation Models Encoded in the MCSim Model Specification Language - Published in JOSS (2025)

Snowdrop — Peer-reviewed • Science 93%

Snowdrop: Python Package for DSGE Modeling - Published in JOSS (2025)

smolyax — Peer-reviewed • Science 98%

smolyax: a high-performance implementation of the Smolyak interpolation operator in JAX - Published in JOSS (2025)

lilyfrogs • Science 67%

56 Lilypads is a turn-based game where frogs leap between lilypads to catch flies and lotuses, but each lilypad disappears once left behind! Compete for the highest score in this strategic battle before movement options run out

Parallel-CDM — Peer-reviewed • Science 98%

Parallel-CDM: Parallel Implementation of Continuum Damage Mechanics Simulations using FEM and MATLAB - Published in JOSS (2025)

ChemInformant — Peer-reviewed • Science 98%

ChemInformant: A Robust and Workflow-Centric Python Client for High-Throughput PubChem Access - Published in JOSS (2025)

collectionbuilder • Science 44%

SDA — Peer-reviewed • Science 93%

SDA: a symbolic differential algebra package in C++ - Published in JOSS (2025)

voice — Peer-reviewed • Science 93%

voice: A Comprehensive R Package for Audio Analysis - Published in JOSS (2025)

BayesReconPy — Peer-reviewed • Science 93%

BayesReconPy: A Python package for forecast reconciliation - Published in JOSS (2025)

SOAP — Peer-reviewed • Science 93%

SOAP: A Python Package for Calculating the Properties of Galaxies and Halos Formed in Cosmological Simulations - Published in JOSS (2025)

PolytopeWalk — Peer-reviewed • Science 93%

PolytopeWalk: Sparse MCMC Sampling over Polytopes - Published in JOSS (2025)

The Population Synthesis Toolkit (PST) Python Library — Peer-reviewed • Science 98%

The Population Synthesis Toolkit (PST) Python Library - Published in JOSS (2025)

PyStarshade — Peer-reviewed • Science 93%

PyStarshade: Simulating High-Contrast Imaging of Exoplanets with Starshades - Published in JOSS (2025)

PAAT — Peer-reviewed • Science 93%

PAAT: Physical Activity Analysis Toolbox for the analysis of hip-worn raw accelerometer data in Python - Published in JOSS (2025)

get_kmers • Science 44%

Get kmers with jellyfish