kaishumason / NicheDE
NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
☆14Updated 4 months ago
Related projects: ⓘ
- Mosaic single cell data integration using non-overlapping features☆34Updated last year
- scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference☆36Updated 2 months ago
- Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression☆21Updated 9 months ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆50Updated 2 months ago
- ☆39Updated 3 years ago
- ☆11Updated 2 years ago
- A manually curated database of literature-supported ligand-receptor interactions in human and mouse☆25Updated 2 months ago
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆21Updated 3 months ago
- R package for detection of cell-cell interaction using Non-negative Tensor Decomposition☆32Updated last year
- ☆11Updated last year
- ☆35Updated last month
- ☆12Updated last year
- General notes and resources on how to analyze Spatial Transcriptomics data☆11Updated last year
- Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and…☆33Updated last year
- R package for pathway analysis in scRNA-seq data☆57Updated last month
- Unsupervised Inference of Developmental Directions for Single Cells☆20Updated 8 months ago
- Identify genes with spatial expression trends in single-cell gene expression data☆47Updated 6 years ago
- Independent Component Analysis decipher functional modules for better cell clustering and annotation☆15Updated 2 years ago
- Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)☆22Updated 3 months ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆39Updated 2 years ago
- ☆44Updated last year
- Functional Inference of Gene Regulation☆33Updated 2 months ago
- Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3☆38Updated 6 months ago
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆45Updated 11 months ago
- Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.☆39Updated this week
- ☆44Updated last month
- psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels☆36Updated 2 years ago
- R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)☆8Updated last year
- ☆13Updated this week
- RNA-velocity informed embeddings for visualizing cellular trajectories☆41Updated 2 years ago