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Single-cell analysis in Python. Scales to >100M cells.
python data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata scverse
Annotated data.
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
scrna-seq shiny-apps single-cell shinyapps single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq seurat single-cell-omics scrna-seq-analysis single-cell-sequencing shiny-app scanpy scatac-seq anndata scrna-pipeline seurat-objects single-cell-pipeline
Cell type annotation for single-cell RNA-seq using multi-LLM consensus
bioinformatics computational-biology single-cell consensus-algorithm scrna seurat scanpy cell-type-annotation large-language-models llm scrnaseq-analysis
scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial data in an easy and efficient way.
visualization spatial-data spatial-data-analysis single-cell-rna-seq giotto single-cell-analysis seurat single-cell-sequencing scanpy
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
visualization python data-science bioinformatics genomics physics heatmap data-visualization scientific-visualization matplotlib plotting chemoinformatics single-cell upset sequence-logo scanpy oncoprint upset-plot complex-heatmap annotated-heatmap
muon is a multimodal omics Python framework
muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata scverse
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
Convert between AnnData and SingleCellExperiment
Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports
Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data
rna-seq transcriptomics single-cell marker-genes disease-prediction scanpy anndata celltype-annotation llm celltype-identification llm-agent agentic-ai cell-state-prediction
Learning cell communication from spatial graphs of cells
tensorflow glm cvae encoder-decoder-model gnn scanpy cell-cell-interaction cell-cell-communication squidpy
BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.
python bioinformatics clustering spatial-analysis spatial-clustering spatial-data-analysis spatial-transcriptomics scanpy spatial-omics
Bring your single-cell data to life
visualization webgl bioinformatics spatial data-visualization scrna-seq transcriptomics single-cell 10x smartseq2 seurat scanpy anndata
Autonomous multi-agent framework to optimize scientific software
python bioinformatics acceleration genomics scientific-computing rstats scrna-seq single-cell speedup code-optimization performance-optimization ai-agents seurat spatial-transcriptomics scanpy llm agentic-ai
MCP server for spatial transcriptomics analysis through natural language interfaces.
visualization python machine-learning bioinformatics genomics computational-biology pytorch spatial-analysis single-cell deconvolution spatial-transcriptomics scanpy spatial-domains squidpy llm-agent cell-communication claude-desktop agentic-ai model-context-protocol mcp-server
pseudobulking on an AnnData object
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
python bioinformatics computational-biology single-cell deconvolution spatial-transcriptomics scanpy visium cell-type-deconvolution
Cell Analyzer for Flow Experiment
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