scanpy

scverse/anndata

Annotated data.

zhanghao-njmu/SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

cafferychen777/mLLMCelltype

🏆 #1 Multi-LLM consensus framework | 550+ stars | 95% accuracy | 10+ LLM providers | Leading cell annotation tool

scverse/muon

muon is a multimodal omics Python framework

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.

CelVoxes/ceLLama

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

theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

theislab/ncem

Learning cell communication from spatial graphs of cells

lilab-bcb/cirrocumulus

Bring your single-cell data to life

NygenAnalytics/CyteType

Multi-agent driven cell type annotation for single-cell RNA-Seq data stored in Anndata format

noamteyssier/adpbulk

pseudobulking on an AnnData object

stefanpeidli/mousipy

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

buettnerlab/pytometry_legacy

This repository extends scanpy to handle flow and mass cytometry data.

gozsari/Single-Cell-Data-Analysis

Notes and studies about single-cell RNA-Seq analysis

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.

ebi-gene-expression-group/scanpy-workflow

Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow

YosefLab/treedata

anndata with trees

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.

mhbsiam/cafe

Cell Analyzer for Flow Experiment

NKI-CCB/sobolev_alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

shahrozeabbas/neutrophil-temporal-analysis

Single-cell temporal analysis of neutrophils using DRVI

SindiLab/ACTINN-PyTorch

An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)

viktormiok/scRNAseq_AdipocyteSubtyping

Python pipelines for analysis of adipocyte scRNA-seq data

lihuax-lab/Juscan.jl

Single-cell data analysis toolkit built with Julia and inspired by Scanpy.

Nuwa-genomics/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

theislab/scanpy-demo-czbiohub

single-cell scanpy teaching

czbiohub-sf/grassp

GRaph-based Analysis of Subcellular/Spatial Proteomics

gambalab/scRNAseq_chapter

Review on Single Cell RNA-sequencing

PMBio/mudatasets

Multimodal datasets, in MuData format

YosefLab/pycea

scverse lineage tracing analysis toolkit

becavin-lab/checkatlas

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

connerlambden/Cube

Intuitive Nonparametric Gene Network Search Algorithm

Iwo-K/genespector

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

Integration analysis with Scanpy and scRNAseq TME from blueprint

mcrewcow/BaranovLab

Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School