GitHub
https://github.com/cosbidev/ostransformer
Official implementation for the paper ``A Deep Learning Approach for Overall Survival Prediction in Lung Cancer with Missing Values´´
https://github.com/corybrunson/ordr
manage ordinations and render biplots in a tidyverse workflow
momepy
momepy: Urban Morphology Measuring Toolkit - Published in JOSS (2019)
PressureDrop.jl
PressureDrop.jl: Pressure traverses and gas lift analysis for oil & gas wells - Published in JOSS (2019)
https://github.com/computational-biology-aachen/synechocystis-photosynthesis-2024
A mathematical model of photosynthetic electron transport in Synechocystis sp. PCC 6803
https://github.com/compiler-campusminden/cpl-vorlesung-master-w25
Lecture "Concepts of Programming Languages" (M.Sc.) (Winter 2025/26)
https://github.com/comp-physics/meshfreetrixi.jl
Meshfree extension to Trixi using RBF-based numerics
https://github.com/coin-or/symphony
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/coderefinery/testing
Automated testing - Preventing yourself and others from breaking your functioning code
https://github.com/cmendl/rqcopt_hpc
HPC implementation of Riemannian quantum circuit optimization
https://github.com/climatecompatiblegrowth/geo-x-data-prep
Spatial data preparation tools for GeoH2 users.
https://github.com/climate-service-center/dacstore
Acceptance analysis DACStorE
https://github.com/cidgoh/nf-ncov-voc
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/chakravala/staticvectors.jl
Statically sized tuple vectors for Julia
https://github.com/ch-earth/openfews
Open and Shareable Delft-FEWS configuration for connecting the Next Generation of Forecasting Tools
https://github.com/cgeoga/vecchia.jl
Vecchia approximations for Gaussian log-likelihoods
https://github.com/centre-for-humanities-computing/llm-tweet-classification
Classifying tweets with large language models with zero- and few-shot learning.
https://github.com/ceed/nekrs
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/cdcgov/irma
IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.
https://github.com/camilogarciabotero/biovossencoder.jl
A small Julia package to represent BioSequences as a Voss matrix
https://github.com/caltechlibrary/2020-05-11-swc-online
May 2020 Software Carpentry Workshop
https://github.com/cair/tsetlinmachine
Code and datasets for the Tsetlin Machine
https://github.com/cornell-zhang/hisparse
High-Performance Sparse Linear Algebra on HBM-Equipped FPGAs Using HLS
https://github.com/bueler/glacier-fe-estimate
extend the Falk technique to Stokes glacier models of surface evolution
https://github.com/brugr9/uepluginvolumecreator
Unreal Engine Plugin: Volume Creator – Documentation
RAFF.jl
RAFF.jl: Robust Algebraic Fitting Function in Julia - Published in JOSS (2019)
https://github.com/broadinstitute/pbs-analysis
Scripts for analyzing ChIP-seq and related datatypes with binning and PBS
https://github.com/broadinstitute/profiling-resistance-mechanisms
Predicting pharmacodynamic responses to cancer drugs using cell morphology
desirna
State of the art software for RNA sequence design. The first to solve the Eterna benchmark!
Optimising Light Source Positioning for Even and Flux-Efficient Illumination
Optimising Light Source Positioning for Even and Flux-Efficient Illumination - Published in JOSS (2019)
https://github.com/brainglobe/brainglobe-template-builder
Build unbiased anatomical templates from individual images
https://github.com/brainets/hosi_infogain
Script for "Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning"
https://github.com/bozenne/article-netbenefit-correction
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 ).
https://github.com/bootphon/speech-map
Mean Average Precision over words or n-grams with speech features
https://github.com/boothgroup/vayesta
A Python package for wave function-based quantum embedding
https://github.com/bodenmillergroup/imcdataanalysis
R based workflow for multiplexed imaging data
https://github.com/bioscan-ml/barcodebert
A pre-trained representation from a transformers model for inference on insect DNA barcoding data.
https://github.com/biolink/resource-ingest-guide-schema
A LinkML schema for describing the scope, rationale, and modeling approach for ingesting content from a single source.
https://github.com/bioinfomachinelearning/multicom4
The MULTICOM4 protein structure prediction system developed by the Bioinformatics and Machine Learning Lab at the University of Missouri - Columbia
https://github.com/biodataanalysisgroup/virtual-tutorial-perturbation-modelling
https://github.com/bioconductor/bioconductor-training
Bioconductor teaching and education committee
https://github.com/bio-rsg/oceancolour
Package of custom functions for remote sensing data analysis
https://github.com/bin-cao/shapev
[JMI 2022 | Aggregate 2025] A package for searching equivalent values based on joined SHAP values
https://github.com/berenslab/llm-excess-vocab
Delving into LLM-assisted writing in biomedical publications through excess vocabulary
https://github.com/benny0323/deep-learning-based-mia-tasks
⭐[A Deep Survey] Paper List For Metal Artifact Reduction including traditional and deepl leanring based methods. ℱℯℯ𝓁 𝒻𝓇ℯℯ to contribute!
https://github.com/bblodfon/pdac-efs-bench2024
Feature Selection benchmark and analysis on multi-omics PDAC datasets
https://github.com/baltic-coastal-monitoring-team/geopoint
GeoPOINT – Synthetic Point Generator for Geospatial Applications
hotsub
hotsub: A batch job engine for cloud services with ETL framework - Published in JOSS (2018)
survxai
survxai: an R package for structure-agnostic explanations of survival models - Published in JOSS (2018)
https://github.com/awesomecosmos/aayushi-verma-cv
Aayushi Verma's Curriculum Vitae.
https://github.com/auroradysis/kerrp2p
KerrP2P is a software designed for forward ray tracing in Kerr spacetime. It is specifically tailored to efficiently calculate multiple null geodesics between designated "source" and "observer" points, locate apparent positions of the corresponding images, and quantify their shapes.
bem
bem: modeling for neutron Bragg-edge imaging - Published in JOSS (2018)
https://github.com/astrazeneca/topmodel
Uses simulated time-to-event data to model efficacy by prevalence-adjusted nAb titres using a time-varying Cox model.
https://github.com/assert-kth/vrepair
open science repo of "Neural Transfer Learning for Repairing Security Vulnerabilities in C Code" https://arxiv.org/pdf/2104.08308
https://github.com/chen-yang-liu/git-rsclip
Git-RSCLIP pre-trained on 10 million Remote sensing image-text pairs
GrainSizeTools
GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size - Published in JOSS (2018)
https://github.com/chen-yang-liu/awesome-change-captioning
🔥Collection of resources and papers
https://github.com/arkokupski-wat/subjective_time_as_emergent_information_processing
The Brain's Clock: From the Phoenix Equation to Holographic Consciousness
https://github.com/arkokupski-wat/hypothesis-of-spontaneous-matter-antimatter-conversion
Hypothesis of Spontaneous Matter→Antimatter Conversion at Planck Densities
https://github.com/arkokupski-wat/g1g2-gravity-duality
🌌 G₁/G₂ Gravity Duality: Proves quantum & cosmic gravity are distinct phenomena.
https://github.com/arkokupski-wat/modified-spacetime-hypothesis
The hypothesis treats spacetime not as a passive backdrop for matter, but as an equal partner in physical transformations. The inspiration stems from explosive chemistry—specifically, how the detonation of high-energy materials mixtures) converts condensed matter into expanding gases and energy.
https://github.com/aria-systems-group/regret_synthesis_toolbox
Source code for Regret synthesis for two-player turn-based game played on graphs - ICRA 22
GEM
GEM: A Python package for graph embedding methods - Published in JOSS (2018)
https://github.com/anon0411/decoh_as_codom
Feedback-guided quantum circuits exploring codomain-zero as a structural condition. 구조 형성의 조건으로서 공역 0을 실험하는 피드백 기반 양자 회로.
https://github.com/annahedstroem/sanity-checks-revisited
[NeurIPS XAIA & Springer] Code and notebooks to paper "A Fresh Look at Sanity Checks for Saliency Maps"
Combining a Probability and a Non-Probability Sample in a Capture-Recapture Setting
Combining a Probability and a Non-Probability Sample in a Capture-Recapture Setting - Published in JOSS (2018)
https://github.com/ambco-iscte/jask
A Library for Generating Questions about Learners' Code in Java
Limbo
Limbo: A Flexible High-performance Library for Gaussian Processes modeling and Data-Efficient Optimization - Published in JOSS (2018)
https://github.com/aloncrack7/data-degradation-detector
Library to make stimations on data degradation
https://github.com/aksw/frankgraphbench
The FranKGraphBench is a Framework to allow KG Aware RSs to be benchmarked in a reproducible and easy to implement manner. It was first created on Google Summer of Code 2023 for Data Integration between DBpedia and some standard RS datasets in a reproducible framework.
CLIMLAB
CLIMLAB: a Python toolkit for interactive, process-oriented climate modeling - Published in JOSS (2018)
TSrepr R package
TSrepr R package: Time Series Representations - Published in JOSS (2018)