https://github.com/ccamp83/mu
R package for general statistical analysis of univariate and multivariate data
https://github.com/ccao-data/extract-permits
Script and workflow for permit data extraction
singlefactorgaussian
Bayesian inference of single factor Gaussian model using Stan
https://github.com/ccbr/bioinfo-pf-curie-chip-seq
Nextflow pipeline for ChIP-seq data quality controls and analysis
https://github.com/deepskies/deepdiagnostics
Inference diagnostics for mostly SBI
an-open-science-approach-to-machine-learning
"An Open Science Approach to Machine Learning in Medical and Biological Research talk" in Saudi Data community
technology-data
Compiles assumptions on energy system technologies (e.g. costs and efficiencies) for various years.
https://github.com/deepskies/deepszsim
https://github.com/ccdmb/pante
A pipeline for predicting and masking transposable elements in multiple genomes.
https://github.com/cchdo/cchdo-news
Standalone news component for the front page
si_pritchard_birch_2014
Supplementary information/data for Pritchard & Birch (2014) doi:10.1111/mpp.12210
https://github.com/ccicb/sigstart
Parse Mutation Files to Formats Compatible with Signature Analysis Toolkits
https://github.com/chanind/bootleg
Self-Supervision for Named Entity Disambiguation at the Tail
https://github.com/chaoqiansci/spatial-pggs-any-network
This includes a Matlab function for calculating the critical synergy factor of spatial PGGs on any network structure and Python programs for agent-based simulations.
leafwaxtools
A package for calculating common indices from plant leaf wax distributions and isotopic data
agent-based-evolutionary-game-dynamics
NetLogo models developed in the book "Agent-Based Evolutionary Game Dynamics"
karyopyploter
Package to mimic the functionality of KaryoploteR, but in Python.
https://github.com/chaos-polymtl/machine-learning-tools
Machine learning tools in Python
https://github.com/chaos-polymtl/bio-pinn
Physics-Informed Neural Network to predict the reaction rates of a BIOdiesel process
https://github.com/chaoscodes/propetl
One Network, Many Masks: Towards More Parameter-Efficient Transfer Learning
https://github.com/chaoscodes/untl
EMNLP'2022: Unsupervised Non-transferable Text Classification
https://github.com/chaoscodes/flash-linear-attention
Efficient implementations of state-of-the-art linear attention models in Pytorch and Triton
cartography
Cartography is a Python tool that consolidates infrastructure assets and the relationships between them in an intuitive graph view powered by a Neo4j database.
https://github.com/chaoscodes/mycyclegan
Image-to-image translation in PyTorch (e.g., horse2zebra, edges2cats, and more)
cmipsummary
A summary paper describing climate science MIP history and evolution
https://github.com/chaoscodes/llmspeculativesampling
Fast inference from large lauguage models via speculative decoding
stats-strided-dmaxabssorted
Calculate the maximum absolute value of a sorted double-precision floating-point strided array.
https://github.com/clarin-eric/clarin-drupal-bootstrap-theme
A SASS subtheme for Drupal bootstrap barrio theme.
cvreviewtool
A tool designed to help librarians research self-archiving policies around faculty publications, and aggregate those results in a tidy, edit-able PDF or HTML report that can be sent directly to faculty. For institutions conducting "CV reviews", this workflow likely sounds familiar. The tool is web-based, with a MySQL backend, and pulling in publisher policies via the SHERPA/RoMEO freely available API.
geant4
Geant4 toolkit for the simulation of the passage of particles through matter - NIM A 506 (2003) 250-303
hictkpy
Python bindings for hictk: read and write .cool and .hic files directly from Python
https://github.com/brunomioto/fishtree
The R interface to the Fish Tree of Life
topolow
A physics-inspired R package for robust Euclidean embedding of sparse, non-metric dissimilarity data. Particularly powerful for antigenic cartography and viral evolution tracking, but applicable to any domain with incomplete similarity measurements. Published in *Bioinformatics* (2025).
https://github.com/ionicabizau/vocal-exercises
:sweat: Some scripts for vocal exercises
