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Projects in Awesome Lists tagged with scanpy

A curated list of projects in awesome lists tagged with scanpy .

https://github.com/scverse/scanpy

Single-cell analysis in Python. Scales to >100M cells.

anndata bioinformatics data-science machine-learning python scanpy scverse transcriptomics visualize-data

Last synced: 11 May 2025

https://github.com/celvoxes/cellama

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

celltype large-language-models llm rna-seq scanpy seurat single-cell

Last synced: 07 May 2025

https://github.com/theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

bioconductor jupyter rpy2 scanpy single-cell

Last synced: 16 May 2025

https://github.com/theislab/ncem

Learning cell communication from spatial graphs of cells

cell-cell-communication cell-cell-interaction cvae encoder-decoder-model glm gnn scanpy squidpy tensorflow

Last synced: 11 Oct 2025

https://github.com/noamteyssier/adpbulk

pseudobulking on an AnnData object

anndata differential-expression pseudobulk scanpy

Last synced: 18 Jan 2026

https://github.com/cafferychen777/chatspatial

🧬 Analyze spatial transcriptomics data through natural language conversation. Stop writing code, start having conversations with your data. MCP server for Claude Code and Codex.

agentic-ai bioinformatics cell-communication claude-desktop computational-biology deconvolution genomics llm-agent machine-learning mcp-server model-context-protocol python pytorch scanpy single-cell spatial-analysis spatial-domains spatial-transcriptomics squidpy visualization

Last synced: 02 May 2026

https://github.com/stefanpeidli/mousipy

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

human mouse python scanpy scrna-seq species

Last synced: 05 Mar 2026

https://github.com/cafferychen777/mLLMCelltype

An iterative multi-LLM consensus framework for accurate cell type annotation in single-cell RNA-seq data

bioinformatics cell-type-annotation consensus-algorithm large-language-models llm scanpy seurat single-cell

Last synced: 24 Apr 2025

https://github.com/czbiohub-sf/grassp

GRaph-based Analysis of Subcellular/Spatial Proteomics

anndata proteomics-data-analysis scanpy spatial-proteomics subcellular-localization

Last synced: 10 Feb 2026

https://github.com/cai-lab-at-university-of-michigan/micv

MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.

anndata clustering gene-expression leiden marker-genes pseudotime pseudotime-trajectory scanpy umap-projection

Last synced: 05 May 2026

https://github.com/theislab/scanpy-demo-czbiohub

single-cell scanpy teaching

scanpy single-cell teaching-materials

Last synced: 18 Feb 2026

https://github.com/becavin-lab/checkatlas

One liner tool to check the quality of your single-cell atlases.

control multiqc python quality scanpy seurat single-cell

Last synced: 09 Apr 2026

https://github.com/cafferychen777/flashdeconv

Fast Linear Algebra for Scalable Hybrid Deconvolution of Spatial Transcriptomics

bioinformatics cell-type-deconvolution computational-biology deconvolution python scanpy single-cell spatial-transcriptomics visium

Last synced: 13 Jan 2026

https://github.com/theislab/hpa_reproducibility

Reproducible code for the scRNA-seq analyses in the paper 'The neuroendocrine response to stress at single-cell resolution" by Lopez et al. 2020.

bioinformatics bioinformatics-analysis scanpy scrna-seq scrna-seq-analysis

Last synced: 11 Oct 2025

https://github.com/mouzkolit/neurobeginner

Data Science Beginner Course teached Jan 23

data-science matplotlib pandas python scanpy scrna-seq

Last synced: 06 May 2026

https://github.com/giatraskon/gastric-cancer-scrnaseq-analysis

Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using single‑cell RNA‑seq" by Wang B. et. al, using the raw counts matrix they provide.

average-linkage bioinformatics clustering gastric-cancer gmm-clustering go-annotation leiden-algorithm louvain-algorithm machine-learning marker-gene-identification pca python sc-rna-seq sc-rna-seq-analysis scanpy single-cell-rna-seq spectral-clustering tsne umap ward-linkage

Last synced: 17 May 2026

https://github.com/Naila-Srivastava/scRNASeq-Cardiac-Development

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.

aws-batch aws-s3 cardiac-development cell-type-annotation cloud-bioinformatics computational-biology docker nextflow python scanpy scrna-seq single-cell umap

Last synced: 08 May 2026

https://github.com/hutaobo/cell-gps

Cell-GPS is the Python package and reference implementation for Cophenetic Spatial Topology Embedding (COSTE), a spatial topology analysis framework for spatial omics data.

bioinformatics data-visualization python scanpy single-cell spatial-analysis spatial-omics spatial-transcriptomics visium xenium

Last synced: 07 Jun 2026

https://github.com/kris96tian/sc-rnaseq_analysis

Single-cell RNA data analysis using R (Seurat) , Python (Scanpy), and Julia.

annotations bioinformatics-analysis pca-analysis sc-rna-seq-analysis scanpy seurat singlr umap

Last synced: 05 May 2025

https://github.com/kris96tian/scrna-webapp

Interactive web application for analyzing scRNA-seq data using Scanpy

scanpy scrna-seq-analysis single-cell-rna-seq

Last synced: 26 Oct 2025