scanpy

There are 3 repositories under scanpy topic.

scanpy
scverse / scanpy
Single-cell analysis in Python. Scales to >100M cells.
machine-learning data-science visualize-data transcriptomics bioinformatics scanpy anndata python scverse
Language:Python 2248
scverse / anndata
Annotated data.
scanpy data-science transcriptomics bioinformatics machine-learning scverse anndata
Language:Python 681
zhanghao-njmu / SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
single-cell seurat-objects single-cell-analysis single-cell-rna-seq scrna-pipeline scrna-seq scrna-seq-analysis seurat scanpy anndata single-cell-omics single-cell-sequencing shiny-apps shiny-app shinyapps single-cell-atac-seq single-cell-genomics single-cell-pipeline scatac-seq
Language:R 581
mLLMCelltype
cafferychen777 / mLLMCelltype
🏆 #1 Multi-LLM consensus framework | 550+ stars | 95% accuracy | 10+ LLM providers | Leading cell annotation tool
artificial-intelligence bioinformatics cell-type-annotation claude computational-biology consensus-algorithm deepseek gemini grok large-language-models llm multi-llm-consensus openai openrouter qwen scanpy scrna scrnaseq-analysis seurat single-cell
Language:Python 563
scverse / muon
muon is a multimodal omics Python framework
multimodal-data multimodal-omics-analysis multi-omics anndata scanpy mudata muon scrna-seq scatac-seq cite-seq scverse
Language:Python 253
interactivereport / cellxgene_VIP
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.
scrna-seq cellxgene scanpy visualization seurat svg publication-quality-plots cellxgene-vip
Language:Jupyter Notebook 159
ceLLama
CelVoxes / ceLLama
Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports
celltype llm single-cell large-language-models rna-seq scanpy seurat
Language:R 150
theislab / anndata2ri
Convert between AnnData and SingleCellExperiment
scanpy single-cell bioconductor jupyter rpy2
Language:Python 142
theislab / ncem
Learning cell communication from spatial graphs of cells
tensorflow gnn glm cvae encoder-decoder-model scanpy squidpy cell-cell-communication cell-cell-interaction
Language:Python 113
lilab-bcb / cirrocumulus
Bring your single-cell data to life
scrna-seq visualization single-cell anndata bioinformatics transcriptomics webgl scanpy seurat spatial 10x smartseq2 data-visualization
Language:JavaScript 88
NygenAnalytics / CyteType
Multi-agent driven cell type annotation for single-cell RNA-Seq data stored in Anndata format
anndata celltype-annotation celltype-identification llm-agent marker-genes scanpy single-cell
Language:Python 48
noamteyssier / adpbulk
pseudobulking on an AnnData object
anndata differential-expression pseudobulk scanpy
Language:Python 34
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
Language:Jupyter Notebook 28
buettnerlab / pytometry_legacy
This repository extends scanpy to handle flow and mass cytometry data.
scanpy flow-cytometry mass-cytometry
Language:Jupyter Notebook 9
gozsari / Single-Cell-Data-Analysis
Notes and studies about single-cell RNA-Seq analysis
single-cell python rna-seq-analysis scanpy awesome-list programming-exercises tutorial single-cell-analysis
Language:Python 9
MiCV
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.
gene-expression scanpy pseudotime pseudotime-trajectory marker-genes umap-projection clustering anndata leiden
Language:CSS 7
ebi-gene-expression-group / scanpy-workflow
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow
nextflow scanpy
Language:Nextflow 7
YosefLab / treedata
anndata with trees
bioinformatics data-science scanpy scverse anndata lineage-tracing
Language:Python 7
kullrich / orthomap
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
orthofinder phylostratigraphy scanpy scrna-seq-analysis evolution expression-profiles gene-expression gene-expression-profiles bioinformatics orthomap python tai transcriptome
Language:Python 6
mhbsiam / cafe
Cell Analyzer for Flow Experiment
conda flowcytometry pixi python3 scanpy single-cell streamlit
Language:Python 6
NKI-CCB / sobolev_alignment
Sobolev alignment of deep probabilistic models for comparing single cell profiles
cancer-genomics cell-lines deep-learning gene-expression kernel-machine-learning pre-clinical scanpy scrna-seq scvi-tools single-cell variational-autoencoder clinical drug-response python
Language:Python 6
shahrozeabbas / neutrophil-temporal-analysis
Single-cell temporal analysis of neutrophils using DRVI
python scanpy drvi bioinformatics singlecell
Language:HTML 6
SindiLab / ACTINN-PyTorch
An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)
single-cell scanpy activa actinn automatic-cell-identification pytorch
Language:Python 6
viktormiok / scRNAseq_AdipocyteSubtyping
Python pipelines for analysis of adipocyte scRNA-seq data
scanpy scrna-seq-analysis adipose-tissue
Language:Jupyter Notebook 6
lihuax-lab / Juscan.jl
Single-cell data analysis toolkit built with Julia and inspired by Scanpy.
bioinfomatics data-analysis julia scanpy single-cell
Language:Julia 5
Nuwa
Nuwa-genomics / Nuwa
A bioinformatics web app for single cell RNA seq analysis.
bioinformatics data-science deep-learning scanpy single-cell spatial-transcriptomics streamlit trajectory-inference transcriptomics web-ui squidpy
Language:Python 5
theislab / scanpy-demo-czbiohub
single-cell scanpy teaching
single-cell scanpy teaching-materials
Language:HTML 5
czbiohub-sf / grassp
GRaph-based Analysis of Subcellular/Spatial Proteomics
anndata proteomics-data-analysis scanpy spatial-proteomics subcellular-localization
Language:Python 4
gambalab / scRNAseq_chapter
Review on Single Cell RNA-sequencing
single-cell-rna-seq single-cell-analysis umap lou gf-icf monocle seurat scanpy single-cell-cl
4
PMBio / mudatasets
Multimodal datasets, in MuData format
multimodal-omics multi-omics scrna-seq multiome muon mudata anndata scanpy
Language:Python 4
YosefLab / pycea
scverse lineage tracing analysis toolkit
bioinformatics lineage-tracing scanpy scverse treedata
Language:Python 4
becavin-lab / checkatlas
One liner tool to check the quality of your single-cell atlases.
control quality scanpy seurat single-cell multiqc python
Language:HTML 3
connerlambden / Cube
Intuitive Nonparametric Gene Network Search Algorithm
gene-relationships scanpy network-analysis single-cell-rna-seq gene-network
Language:Python 3
Iwo-K / genespector
scrna-seq anndata scanpy transcriptomics rna-seq
Language:Python 3
luglilab / NaCl-enhances-CD8-T-cell-effector-functions-in-cancer-immunotherapy
Integration analysis with Scanpy and scRNAseq TME from blueprint
scanpy scrnaseq tutorial scrna-seq-analysis scrna-pipeline
Language:Jupyter Notebook 3
mcrewcow / BaranovLab
Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
gsea maturation migration python r retina scanpy scrna-seq scrna-seq-analysis seurat single-cell transcriptomics retinal-ganglion-cell scfates neuron
Language:Jupyter Notebook 3

scanpy

scverse / scanpy

scverse / anndata

zhanghao-njmu / SCP

cafferychen777 / mLLMCelltype

scverse / muon

interactivereport / cellxgene_VIP

CelVoxes / ceLLama

theislab / anndata2ri

theislab / ncem

lilab-bcb / cirrocumulus

NygenAnalytics / CyteType

noamteyssier / adpbulk

stefanpeidli / mousipy

buettnerlab / pytometry_legacy

gozsari / Single-Cell-Data-Analysis

Cai-Lab-at-University-of-Michigan / MiCV

ebi-gene-expression-group / scanpy-workflow

YosefLab / treedata

kullrich / orthomap

mhbsiam / cafe

NKI-CCB / sobolev_alignment

shahrozeabbas / neutrophil-temporal-analysis

SindiLab / ACTINN-PyTorch

viktormiok / scRNAseq_AdipocyteSubtyping

lihuax-lab / Juscan.jl

Nuwa-genomics / Nuwa

theislab / scanpy-demo-czbiohub

czbiohub-sf / grassp

gambalab / scRNAseq_chapter

PMBio / mudatasets

YosefLab / pycea

becavin-lab / checkatlas

connerlambden / Cube

Iwo-K / genespector

luglilab / NaCl-enhances-CD8-T-cell-effector-functions-in-cancer-immunotherapy

mcrewcow / BaranovLab