Repository Index

GeneCompass

Integrated pipeline for multiplexed image analysis

• multiplexed-imaging
• python

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.

:dart: Accurate sums and dot products for Python.

• mathematics
• numerical-methods
• engineering
• accuracy

Cumo (pronounced like "koomo") is CUDA aware numerical library whose interface is highly compatible with Ruby Numo

• ruby
• cuda
• numo
• scicentific-computing

Detecting cancers on mobile phones

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.

Toolbox for the analysis of smFISH images.

• pattern-classification
• rna-localization
• segmentation
• smfish

BulkFormer: A large-scale foundation model for human bulk transcriptomes

python functions for simulating optical transfer functions

• microscopy
• numpy

Variations on Kirby & Paris' hydra battles and other entertaining math in Coq (collaborative, documented, includes exercises) [maintainer=@Casteran]

• coq
• hydra-battles
• ordinal-notations
• formal-proofs

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

• deep-generative-model
• deep-learning
• single-cell-data-integration
• single-cell-multiomics

👩‍💻 Matrix and other math, accelerated by WebGPU and WASM

• webgpu
• deno
• matrix
• machine-learning

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

• epigenomics
• pattern-search
• data-visualization
• interactive-machine-learning

Research experiments exploring uncommon quant techniques.

• analysis
• jupyter-notebook
• python
• quant

A set of protocols for Arithmetic, Statistics and Logical operations

Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications

• cell-annotation
• multiplexed-imaging
• mpif

Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.

• foundation-models
• gpt
• single-cell

Classification and Gradient-based Localization of Chest Radiographs using PyTorch.

• fine-tuning
• vgg16
• resnet18
• densenet121

The repository host gives no description.

C# math expression library with symbolic computation support

• csharp
• dotnet
• expression-parser
• math

Elixir library implementing a parallel matrix multiplication algorithm and other utilities for working with matrices. Used for benchmarking computationally intensive concurrent code.

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations