single-cell-analysis 开源项目推荐（262 个）

sqjin /CellChat

R工具包，用于根据单细胞数据推断、可视化和分析细胞间通信

jinworks /CellChat

R工具包，用于从单细胞和空间分辨转录组学中推断、可视化和分析细胞间通讯

zhanghao-njmu /SCP

端到端单细胞管道，旨在促进单细胞数据的全面分析和探索。

DingWB /PyComplexHeatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

satijalab /seurat-wrappers

Community-provided extensions to Seurat

pwwang /scplotter

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.

r3fang /SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

slowkow /harmonypy

🎼 整合多个高维数据集，采用模糊的k均值和局部线性调整。

quadbio /scRNAseq_analysis_vignette

Tutorial for scRNA-seq data analysis beginners using R

sunduanchen /Scissor

Scissor package

kharchenkolab /numbat

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

p-gueguen /Spatial_transcriptomics_tools

List of Spatial Transcriptomics related Tools organized per category

ikeda042 /PhenoPixel

PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.

integrativebioinformatics /scNotebooks

This repository contains scNotebooks, a collection of interactive Jupyter and Google Colab notebooks designed to teach and practice single‑cell and spatial transcriptomics. The notebooks guide learners through the complete workflow from introductory steps and single‑cell pipelines to diverse analytical approaches, and FAIR and sharing data

pinellolab /dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

dynverse /dynmethods

A collection of 50+ trajectory inference methods within a common interface 📥📤

singleron-RD /CeleScope

Single Cell Analysis Pipelines

GregorySchwartz /too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.

labsyspharm /scimap

Spatial Single-Cell Analysis Toolkit

MannLabs /scPortrait

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images