Repository Index

A performance oriented 2D/3D math package for Go

Image restoration for fluorescence microscopy

Ark -- Archetype-based Entity Component System (ECS) for Go.

• ecs
• entity-component-system
• go
• golang

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

Descriptor computation(chemistry) and (optional) storage for machine learning

Kaapana is an open source toolkit for state of the art platform provisioning in the field of medical data analysis. The applications comprise AI-based workflows and federated learning scenarios with a focus on radiological and radiotherapeutic imaging. The name Kaapana comes from the Hawaiian word kaʻāpana, meaning "distributor" or "part".

• imaging
• ai
• cloud-computing
• medical-imaging

Interactive 2D wave optics simulator. Turn any image into a refractive scene, add sources, watch waves refract, diffract and interfere. Probes, intensity maps, video export.

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

• histology
• wsi-images
• pan-cancer-analysis
• genomics

Ankh: Optimized Protein Language Model

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

Allocators, I/O streams, math, geometry, image and audio processing for D

• utility-library
• dlang
• linear-algebra
• computational-geometry

Graph-based molecule modeling toolkit for cheminformatics

• cheminformatics
• molecular-modeling
• chemistry
• toolkit

talk with NCBI entrez using R

• r
• rstats
• r-package

Umbrella package of the 'spatstat' family................

• r
• spatial-analysis
• spatial-data
• spatstat

A gallery of animations in statistics and utilities to create animations

• r
• r-package
• animation
• statistics

Converts medical images to more displayable formats, e.g. NIfTI to jpg.

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

Medical LLM agent and MRI segmentation workspace built on PharmaLLM, with LangGraph, vLLM, and BEU-Net.

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

• cancer-imaging-research
• radiomics
• radiomics-features
• machine-learning

Associated Repository for "Translation between Molecules and Natural Language"

TranslatedAcademic research library for DSH — search, cite, approve imports, hand off notes. Also: a research literature library plugin for DeepSeek Harness: search papers, include sources, approve imports into the library, and hand off note leads to other plugins in the same session.

• academic
• agentero
• ai-agents
• citations

A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology