cell-type-annotation

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

A Multi-Modal AI Copilot for Single-Cell Analysis with Instruction Following

Unbiased single-cell transcriptomic data cell type identification

OTMODE: An Optimal Transport-Based Framework for Differential Feature Identification in Single-Cell Multi-Omics

graph-based cell type annotation toolkit for single-cell RNA-seq, ATAC-seq, and spatial omics

The official implementation for "SANGO".

cRegulon is an optimization model to identify combinatorial regulon from single cell expression and chromatin accessibility data.

Automated scRNA-seq cell annotation via local LLM

Agent-native, local-first plugin for auditable single-cell annotation with governed evidence, contrastive review, conservative abstention, and human-reviewed draft outputs.

Tutorial and learning materials for CyteTypeR, an R package for automated cell type annotation of scRNA-seq data using the CyteType API.

Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs.

A curated list of tools and methods for scRNA-seq cell type annotation

Hierarchical and high-resolution cell-type identification for single-cell RNA-seq data based on ScType.

This repository contains an analysis pipeline for processing and visualizing single-cell RNA sequencing (scRNA-seq) data using the Seurat package in R. The dataset used is the Peripheral Blood Mononuclear Cells (PBMC) 3K dataset from 10X Genomics.

Single-cell RNA-seq figure replication project demonstrating clustering, dimensionality reduction, and cell-type annotation using Scanpy in Python.

cRegulon is an optimization model to identify combinatorial regulon from single cell expression and chromatin accessibility data.

End-to-end scRNA-seq pipeline mapping 10 cardiac cell types across 11,046 developing heart cells using Scanpy with a cloud-native Nextflow + AWS Batch architecture for scalable deployment.

Agentic single-cell RNA-seq analysis system for 10x Genomics Chromium

Python wrapper for Azimuth single-cell reference mapping: annotate cell types from AnnData using rpy2

scRNA-seq-navigator is a post-alignment pipeline that utilizes Scanpy for data processing and scANVI and CellTypist for cell type annotations.