spacexr

Transcriptomics analysis tool

Software package for cell type identification and differential expression in spatial transcriptomics

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

GitHub

322 stars
10 watching
73 forks
Language: HTML
last commit: 8 months ago
cell-type-identificationdifferential-expressionspatial-transcriptomics

Related projects:

Repository Description Stars
teichlab/spatialde Tools and methods to analyze gene expression data in relation to spatial coordinates 151
su-informatics-lab/dstg Software implementation of graph-based AI method for decomposing spatial transcriptomics data 35
zjufanlab/spatalk An R package that infers cell-cell communication and ligand-receptor-target networks from spatially resolved transcriptomic data 61
zjufanlab/scdeepsort A tool for accurately annotating cell types in single-cell RNA sequencing data using deep learning 100
qifeidkn/stagate A software framework for learning spatial embeddings from high-dimensional transcriptomics data using an adaptive graph attention auto-encoder 41
aertslab/cistopic An R package for identifying cell states and cis-regulatory topics from single-cell epigenomics data 135
imb-computational-genomics-lab/ascend Tools and methods for analyzing single-cell RNA sequencing data, including expression normalization and differential gene expression analysis. 22
kstreet13/bioc2020trajectories Analyzing and comparing single-cell RNA-seq data across multiple conditions to infer cell trajectories and detect differential expression. 25
hms-dbmi/scde Provides statistical methods for analyzing single-cell RNA-seq data, focusing on error modeling and differential expression analysis. 173
mathewchamberlain/signacx Classifies cellular phenotype in single-cell RNA sequencing data using neural networks 24
ucarlab/iasva Analyzes correlated hidden factors from single-cell transcriptomes to identify biological variation 8
scverse/scvi-tools Probabilistic analysis tools for single-cell omics data 1,270
swainasish/spatialprompt A software tool for analyzing spatial transcriptomics data by separating cell types from location information 12
zjufanlab/sccatch Automated tool for annotating cell types from single-cell RNA sequencing data based on marker genes 219
immcore/is-cellr A web-based Shiny application for analyzing single-cell RNA sequencing data 23