GitHub
appian
APPIAN is an open-source automated software pipeline for analyzing PET images in conjunction with MRI. The goal of APPIAN is to make PET tracer kinetic data analysis easy for users with moderate computing skills and to facilitate reproducible research.
aiproteomics
A package for MSMS spectral library prediction models from the field of (phospho-)proteomics, intended to facilitate the testing and comparison of different neural network architectures and existing models.
doi-exercise
Repository to train making a GitHub repository public following these instruction: https://coderefinery.github.io/github-without-command-line/doi/ which are part of this repository by coderefinery: https://github.com/coderefinery/github-without-command-line
tiledmultigpuvisualization
Using tiled display systems for the interactive visualization of GPGPU computed data
ed-lgt
Code for Exact Diagonalization of Quantum Many-Body Hamiltonians and Lattice (Abelian and Non-Abelian) Gauge Theories in D=1,2,3 spatial dimensions
integrate-indicator-software
Scripts to explore the streamlining and integration of software (with focus on R packages) related to the calculation of indicators based on biodiversity data cubes
ar7-wg1-fod-ch99-fig99-python
example, base on ar6 chapter3 figure11, https://github.com/IPCC-WG1/Chapter-3_Fig11
volume-cartographer
Volumetric processing toolkit and C++ libraries for the recovery and restoration of damaged cultural materials
https://github.com/inutano/rsem
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
fluidimage
:sparkler: A libre Python framework for scientific treatments of large series of images (publish-only mirror)
glamod-marine-processing
Code and configuration for GLAMOD marine data processing
lc-containers_vms
Library Carpentry Containers and Virtual Machines for Librarians
notch-delta-coupling
Source code for "Coupling dynamics of 2D Notch-Delta signalling", by Francisco Berkemeier and Karen M. Page
faser-2-mphys-project-acts
My edits to the ACTS simulation software for simulating background radiation in the FASER-2 detector.
https://github.com/ivis-at-bilkent/cytoscape.js-cose-bilkent
The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement.
mech-m-dual-1-dbm
Course material for a ~3 * 15 hours (5 ECTS) course on basic concepts for data science. All the topics are presented with the Python implementation included. We cover matrix decompositions, regression, signal processing, sparsity and compressed sensing and a bit of statistics.
https://github.com/inutano/pitagora-cwl
Common Workflow Language tools and workflows by Pitagora-Network
m4fsdp
Output routines for extracting results from the MAgPIE framework (versions 4.x) for the FSDP project
burgers-vector-calculator
Program that computes Burgers vectors from elastic strain and lattice rotation data
intro-bayesian-statistics-training
SIB course on bayesian statistics with applications using Rstan
anomalydetector
Intelligent Surveillance System Using Motion Anomaly Detection
stats-strided-wasm-dmeanwd
Calculate the arithmetic mean of a double-precision floating-point strided array using Welford's algorithm.
installkernel-wsl
Script and installkernel hook to copy Linux kernel to the host system and update .wslconfig.
fair-convergence-matrix
Basic code to create FAIR convergence matrix from nanodash nanopublications
sequencecomposition
Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition
neuco-bench
Welcome to NeuCo-Bench, a benchmarking framework for evaluating compressed embeddings on downstream tasks.
pmv-si-2023-2-pe1-t2-house-hero
pmv-si-2023-2-pe1-t2-house-hero created by GitHub Classroom
https://github.com/ivorytower152/denoising-diffusion-pytorch
Implementation of Denoising Diffusion Probabilistic Model in Pytorch
eista
A single-cell spatial transcriptomics pipeline aimed at covering all analysis stages from quantification and clustering to tertiary analyses.
lkfmixer
LKFMixer: Exploring Large Kernel Feature For Efficient Image Super-Resolution
https://github.com/boyle-lab/gpatch-manuscript
Data retrieval and Analysis steps for the GPatch manuscript.
presentation.template
This repository contains latex templates for NumPEx documents
neuropyxels
NeuroPyxels (npyx) is a python library built for electrophysiologists using Neuropixels electrodes. This package stems from the need of a pythonist who really did not want to transition to MATLAB to work with Neuropixels: it features a suite of core utility functions for loading, processing and plotting Neuropixels data.
ssp-mmc
A Stochastic Shortest Path Algorithm for Optimizing Spaced Repetition Scheduling
recoll
Recoll is a desktop full-text search tool (forked from the original at framagit)
https://github.com/ivorytower152/mmpose
OpenMMLab Pose Estimation Toolbox and Benchmark.
aises-virtue-ethics
Teach virtue ethics to AI, an alternative approach to ConstitutionalAI. Final project for the AISES course, fall 2025
