Tangram

Gene mapping tool

A Python package for aligning single-cell transcriptomic data with spatial gene expression data.

Spatial alignment of single cell transcriptomic data.

GitHub

258 stars
13 watching
51 forks
Language: Jupyter Notebook
last commit: 5 months ago
computational-biologygene-expressionscrna-seqsnrna-seqspatial-datavisium

Related projects:

Repository Description Stars
teichlab/spatialde Tools and methods to analyze gene expression data in relation to spatial coordinates 145
qifeidkn/stagate A software framework for learning spatial embeddings from high-dimensional transcriptomics data using an adaptive graph attention auto-encoder 37
raphael-group/paste2 A software framework for aligning and reconstructing spatial transcriptomics data from non-overlapping samples 29
su-informatics-lab/dstg Software implementation of graph-based AI method for decomposing spatial transcriptomics data 34
gao-lab/slat A software package for aligning single-cell spatial omics data using deep learning and graph neural networks 80
raphael-group/paste A method for aligning and integrating spatial transcriptomics data by leveraging both gene expression similarity and spatial distances 78
kharchenkolab/numbat Analyzes single-cell RNA-seq data to detect allele-specific copy number variations and infer lineage relationships in cancer cells 166
scverse/scanpy A Python toolkit for analyzing large-scale single-cell gene expression data 1,919
fridleylab/spatialge A software package for analyzing and visualizing spatial gene expression data from single-cell RNA sequencing assays. 13
dmcable/spacexr Software package for cell type identification and differential expression in spatial transcriptomics 312
edward130603/bayesspace A Bayesian model for clustering and enhancing spatial gene expression data 111
zhoux85/staligner Tool for aligning and integrating spatially resolved transcriptomics data using machine learning algorithms 29
jamesjcai/scgeatoolbox A toolset for analyzing single-cell gene expression data from RNA sequencing experiments. 24
zjufanlab/spatalk An R package that infers cell-cell communication and ligand-receptor-target networks from spatially resolved transcriptomic data 62
rajewsky-lab/novosparc Software tool to predict spatial locations of single cells in tissue using single-cell RNA sequencing data 126