spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
sntools
sntools: An event generator for supernova burst neutrinos - Published in JOSS (2021)
wikes-toolkit
a user-friendly toolkit for the Wiki-Entity-Summarization (WikES) project.
https://github.com/cytoscape/cytoscape.js-klay
The Klay layout algorithm for Cytoscape.js
GRDzhadzha
GRDzhadzha: A code for evolving relativistic matter on analytic metric backgrounds - Published in JOSS (2024)
glotzerlab_citations
Collection of citations commonly used in papers in the Glotzer group
gwaihir
Repository regarding the Gwaihir GUI used for Bragg Coherent Coherent Diffraction (BCDI) data analysis
track2KBA
An R package that facilitates the identification of animal aggregations of potential conservation significance based on individual tracking data. Key functions include utilities to identify and summarise individual foraging trips, estimate utilisation distributions, and overlay distributions to identify important aggregation areas.
Spine-Toolbox
Spine Toolbox is an open source Python package to manage data, scenarios and workflows for modelling and simulation. You can have your local workflow, but work as a team through version control and SQL databases.
https://github.com/csoneson/alevinqc
Create QC and summary reports for Alevin output
kb-python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
d3heatmap
d3heatmap is a Python package to create interactive heatmaps based on d3js.
cppnumericalsolvers
a lightweight header-only C++17 library of numerical optimization methods for (un-)constrained nonlinear functions and expression templates
necsim-rust
Spatially explicit biodiversity simulations using a parallel library written in Rust
lidar
lidar: A Python package for delineating nested surface depressions from digital elevation data - Published in JOSS (2021)
QuadraticModels
Data structures for linear and quadratic optimization problems based on NLPModels.jl
MicrobiomeProfiler
:microbe: A shiny package for microbiome functional enrichment analysis
cosraymodifiediso
A Python library for acquiring galactic cosmic ray spectra at Earth from the ISO model as modified by DLR. All the details and equations about this model can be found in Matthiae et al., A ready-to-use galactic cosmic ray model, Advances in Space Research 51.3 (2013): 329-338, https://doi.org/10.1016/j.asr.2012.09.022 .
h2o
H2O is an Open Source, Distributed, Fast & Scalable Machine Learning Platform: Deep Learning, Gradient Boosting (GBM) & XGBoost, Random Forest, Generalized Linear Modeling (GLM with Elastic Net), K-Means, PCA, Generalized Additive Models (GAM), RuleFit, Support Vector Machine (SVM), Stacked Ensembles, Automatic Machine Learning (AutoML), etc.
autodistill
Images to inference with no labeling (use foundation models to train supervised models).
aeolus
Analysis and visualisation of atmospheric model output powered by iris.
https://github.com/biopragmatics/pyobo
📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures
rage
R tools for performing ageing focussed analyses using matrix population models.
clim-recal
Open repository of methods for recalibrating & bias correcting UKCP18 climate projections data
agent-model-integration
Integration of an Agent Model into an Open Simulation Architecture for Scenario-Based Testing of Automated Vehicles
https://github.com/doi-usgs/loadflex
Models and Tools for Watershed Flux Estimates
marimo
Transform data, train models, and run SQL with marimo — feels like a next-gen reactive notebook, stored as Git-friendly reproducible Python. Deploy as scripts, pipelines, endpoints, and apps. All from an AI-native editor (or your own).
https://github.com/yesint/molar
Repository for molar crate and its dependencies
morl-baselines
Multi-Objective Reinforcement Learning algorithms implementations.
beautier
R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
boutiques
A cross-platform descriptive command-line framework for applications
flowkit
A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
gridit
Provides spatial tools to translate raster or vector polygon data to regular grids
divbrowse
A web application for interactive visualization and exploratory data analysis of variant call matrices
stellarium
Stellarium is a free GPL software which renders realistic skies in real time with OpenGL. It is available for Linux/Unix, Windows and macOS. With Stellarium, you really see what you can see with your eyes, binoculars or a small telescope.
TargetSearch
R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.
deeppurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
reproducibility_in_plant_pathology
A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.
basedosdados
⚙️ Código de manutenção do datalake (metadados e pacotes de acesso) | 📖 Docs: https://basedosdados.org/docs/home
ECNet
ECNet: Large scale machine learning projects for fuel property prediction - Published in JOSS (2017)
@stdlib/blas-ext-base-gsumkbn
Calculate the sum of strided array elements using an improved Kahan–Babuška algorithm.
cspstandsegmentation
R package for single tree delination from TLS/MLS/ULS point clouds
spanner
Utilities to support landscape-, forest-, and tree-related data collection, manipulation, analysis, modelling, and visualization.
https://github.com/antsx/antspymm
utilities for processing modalities beyond T1w
pyiron_gui
Extended graphical user interface (GUI) for pyiron the integrated development environment (IDE)
