xzhoulab / SPARK
Spatially resolved transcriptomic analysis
☆54Updated 2 years ago
Alternatives and similar repositories for SPARK:
Users that are interested in SPARK are comparing it to the libraries listed below
- ☆114Updated 2 years ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- Single cell omics biology annotations☆50Updated last month
- Methods to compute Local Inverse Simpson's Index (LISI)☆61Updated 3 years ago
- Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition☆56Updated 10 months ago
- Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.☆67Updated last month
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆67Updated 2 years ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆68Updated last month
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆89Updated this week
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆60Updated 10 months ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆47Updated last week
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆51Updated 5 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 8 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆62Updated 2 weeks ago
- Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets☆30Updated last year
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆63Updated last month
- BANKSY: spatial clustering☆89Updated 7 months ago
- ☆49Updated 5 months ago
- R package for pathway analysis in scRNA-seq data☆69Updated 6 months ago
- Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…☆39Updated 3 years ago
- Identify genes with spatial expression trends in single-cell gene expression data☆50Updated 6 years ago
- Analysis of cell-cell communication at single-cell resolution☆100Updated 5 months ago
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆56Updated this week
- Metacells - Single-cell RNA Sequencing Analysis☆101Updated 5 months ago
- CeLEry: cell location recovery in single-cell RNA sequencing☆33Updated 2 weeks ago
- R implementation of GeneTrajectory☆53Updated 10 months ago
- An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)☆35Updated 6 months ago
- Methods to discover gene programs on single-cell data☆102Updated 3 months ago
- Spatial mapping of cell types by integration of transcriptomics data☆89Updated 2 years ago
- Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data☆65Updated last month