scanpy

There are 3 repositories under scanpy topic.

scanpy
scverse / scanpy
Single-cell analysis in Python. Scales to >100M cells.
anndata bioinformatics data-science machine-learning python scanpy scverse transcriptomics visualize-data
Language:Python 2061
scverse / anndata
Annotated data.
anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics
Language:Python 614
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 559
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 247
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 157
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 147
theislab / anndata2ri
Convert between AnnData and SingleCellExperiment
bioconductor jupyter rpy2 scanpy single-cell
Language:Python 132
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 112
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 79
noamteyssier / adpbulk
pseudobulking on an AnnData object
anndata differential-expression pseudobulk scanpy
Language:Python 29
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 20
buettnerlab / pytometry_legacy
This repository extends scanpy to handle flow and mass cytometry data.
scanpy flow-cytometry mass-cytometry
Language:Jupyter Notebook 9
ebi-gene-expression-group / scanpy-workflow
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow
nextflow scanpy
Language:Nextflow 7
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 7
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 6
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
SindiLab / ACTINN-PyTorch
An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)
actinn activa automatic-cell-identification pytorch scanpy single-cell
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 5
theislab / scanpy-demo-czbiohub
single-cell scanpy teaching
single-cell scanpy teaching-materials
Language:HTML 5
viktormiok / scRNAseq_AdipocyteSubtyping
Python pipelines for analysis of adipocyte scRNA-seq data
scanpy scrna-seq-analysis adipose-tissue
Language:Jupyter Notebook 5
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
zehua0417 / Juscan.jl
Single-cell data analysis toolkit built with Julia and inspired by Scanpy.
bioinfomatics data-analysis julia scanpy single-cell
Language:Julia 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-network gene-relationships network-analysis scanpy single-cell-rna-seq
Language:Python 3
Iwo-K / genespector
anndata rna-seq scanpy scrna-seq transcriptomics
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
Nuwa
Nuwa-genomics / Nuwa
A bioinformatics web app for single cell RNA seq analysis.
bioinformatics data-science deep-learning scanpy single-cell spatial-transcriptomics squidpy streamlit trajectory-inference transcriptomics web-ui
Language:Python 3
YosefLab / treedata
anndata with trees
bioinformatics data-science scanpy scverse anndata lineage-tracing
Language:Python 3
AseenaSulthana / Cyber-Archive
Recon Automation Tool is a Python-based toolkit designed for web penetration testing and reconnaissance. It features IP and port scanning, barcode and QR code generation, password and wordlist creation, phone number information gathering, subdomain checking, and even a DDoS attack simulation tool. Ideal for security professionals.
ddos-attacks dns network-scanning python scanpy
Language:Python 2
liekevandehaar / Dev_Hb_mouse
Transcriptomic analysis of the developing mouse habenula
correlation gwas habenula mouse scrna-seq brain correlation-analysis scanpy seurat
Language:Jupyter Notebook 2
lisafournier / GenomicsProject
Analysis of a .loom file containing single-cell RNA-sequencing data. Clustering & UMAP embedding using Scanpy, followed by RNA velocity analysis using scVelo.
single-cell-rna-seq scanpy scvelo
Language:Jupyter Notebook 2
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 neuron python r retina retinal-ganglion-cell scanpy scfates scrna-seq scrna-seq-analysis seurat single-cell transcriptomics
Language:Jupyter Notebook 2
mhbsiam / cafe
Cell Analyzer for Flow Experiment
conda flowcytometry pixi python3 scanpy single-cell streamlit
Language:Python 2
milescsmith / s2a
Seurat to AnnData conversion
seurat anndata scanpy
Language:Python 2
PMBio / mudatasets
Multimodal datasets, in MuData format
multimodal-omics multi-omics scrna-seq multiome muon mudata anndata scanpy
Language:Python 2
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
Language:Jupyter Notebook 2

scanpy

scverse / scanpy

scverse / anndata

zhanghao-njmu / SCP

scverse / muon

interactivereport / cellxgene_VIP

CelVoxes / ceLLama

theislab / anndata2ri

theislab / ncem

lilab-bcb / cirrocumulus

noamteyssier / adpbulk

stefanpeidli / mousipy

buettnerlab / pytometry_legacy

ebi-gene-expression-group / scanpy-workflow

gozsari / Single-Cell-Data-Analysis

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

kullrich / orthomap

SindiLab / ACTINN-PyTorch

NKI-CCB / sobolev_alignment

theislab / scanpy-demo-czbiohub

viktormiok / scRNAseq_AdipocyteSubtyping

gambalab / scRNAseq_chapter

zehua0417 / Juscan.jl

becavin-lab / checkatlas

connerlambden / Cube

Iwo-K / genespector

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

Nuwa-genomics / Nuwa

YosefLab / treedata

AseenaSulthana / Cyber-Archive

liekevandehaar / Dev_Hb_mouse

lisafournier / GenomicsProject

mcrewcow / BaranovLab

mhbsiam / cafe

milescsmith / s2a

PMBio / mudatasets

theislab / HPA_reproducibility