squidpy

Spatial analysis library

A Python library for analyzing and visualizing spatial molecular data from single-cell genomics and tissue images

Spatial Single Cell Analysis in Python

GitHub

447 stars
10 watching
83 forks
Language: Python
last commit: 1 day ago
Linked from 1 awesome list

data-visualizationimage-analysissingle-cell-genomicssingle-cell-rna-seqspatial-analysisspatial-transcriptomicssquidpy

Backlinks from these awesome lists:

Related projects:

Repository Description Stars
scverse/scanpy A Python toolkit for analyzing large-scale single-cell gene expression data 1,942
scverse/scvi-tools Probabilistic analysis tools for single-cell omics data 1,263
scverse/scirpy Analyzes single-cell TCR and BCR data from scRNA-seq using Python 222
dataverselabs/pyinterpolate A Python package for performing spatial interpolation and analysis using various techniques 157
rabadanlab/sctda An object-oriented Python library for analyzing single-cell RNA-seq data using topological representations 7
pysal/pysal A comprehensive Python library for geospatial data science and analysis, providing tools for spatial statistics, graph construction, and exploratory data analysis. 1,346
rraadd88/htsimaging A Python package for analyzing high-throughput single-cell imaging data 5
qifeidkn/stagate A software framework for learning spatial embeddings from high-dimensional transcriptomics data using an adaptive graph attention auto-encoder 39
cbib/dypfish A Python library for statistical analysis of mRNA and protein distributions in single cell confocal images 2
quant-aq/py-smps A Python library for analyzing and visualizing data from various aerosol sizing instruments 32
makepath/xarray-spatial A Python library for efficient raster analysis and processing of spatial data 848
earthlab/earthpy A Python package for simplifying spatial data manipulation and analysis 512
euxhenh/cellar An interactive software tool for analyzing single-cell omics data 32
fish-quant/big-fish A toolbox for analyzing microscopy images of cells labeled with single-molecule fluorescent in situ hybridization (smFISH) tags. 58
xmc811/scillus A package for processing and visualizing single-cell RNA-seq data in R, providing an efficient and customizable framework for analyzing complex biological datasets. 59