xzhoulab / SPARKLinks
Spatially resolved transcriptomic analysis
☆55Updated 2 years ago
Alternatives and similar repositories for SPARK
Users that are interested in SPARK are comparing it to the libraries listed below
Sorting:
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆74Updated 2 years ago
- Methods to compute Local Inverse Simpson's Index (LISI)☆61Updated 3 years ago
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆74Updated 6 months ago
- R package for pathway analysis in scRNA-seq data☆73Updated 9 months ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆66Updated last month
- Python implementation of Milo for differential abundance testing on KNN graph☆68Updated 3 months ago
- CAST package☆40Updated 7 months ago
- ☆28Updated 3 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
- Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition☆60Updated last year
- ☆25Updated 3 months ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆52Updated last month
- Integrative and Reference-Informed Spatial Domain Detection for Spatial Transcriptomics☆35Updated 4 months ago
- Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.☆74Updated last month
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆42Updated 3 years ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆68Updated last month
- TACCO: Transfer of Annotations to Cells and their COmbinations☆48Updated 10 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆70Updated 2 years ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆73Updated 4 months ago
- Single cell omics biology annotations☆51Updated last month
- Single-cell Lung Cancer Atlas with 1.2M cells☆63Updated 4 months ago
- scPred package for cell type prediction from scRNA-seq data☆89Updated last year
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 11 months ago
- ☆119Updated 3 years ago
- Bayesian Analytics for Spatial Segmentation☆28Updated last month
- Spatial Cellular Estimator for Tumors☆51Updated 2 weeks ago
- Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper☆47Updated 4 months ago
- Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets☆30Updated last year
- PhyloVelo, Phylogeny-based transcriptomic velocity of single cells☆43Updated last year
- Construct Tumor Transition Zone Microenvironment☆42Updated 6 months ago