raphael-group / CalicoSTLinks
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
☆41Updated 2 months ago
Alternatives and similar repositories for CalicoST
Users that are interested in CalicoST are comparing it to the libraries listed below
Sorting:
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆27Updated last year
- Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition☆61Updated last year
- Aligning gene expression trajectories of single-cell reference and query systems☆76Updated 2 months ago
- We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and ti…☆13Updated last year
- cell type specific, trait-associated gene regulation☆29Updated 6 months ago
- Cell age determination by scATAC-seq and bulk-ATAC-seq☆32Updated last year
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆33Updated last year
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 3 years ago
- ☆31Updated 3 months ago
- Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression☆29Updated 10 months ago
- ☆53Updated 2 years ago
- Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020☆18Updated 2 years ago
- ☆23Updated 2 years ago
- ☆59Updated 4 months ago
- ☆58Updated last month
- ☆30Updated 5 months ago
- ☆45Updated last year
- Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)☆32Updated 9 months ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Updated 9 months ago
- ☆32Updated 9 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆66Updated 3 weeks ago
- This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…☆26Updated last year
- Multi-resolution Variational Inference☆22Updated last week
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆56Updated 5 months ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆80Updated 7 months ago
- Independent Component Analysis decipher functional modules for better cell clustering and annotation☆17Updated 3 years ago
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆22Updated 4 months ago
- sEV-containing droplet identification in scRNA-seq data (SEVtras)☆26Updated 8 months ago
- Cell-type Relationship Analysis Workflow Done Across Distances☆38Updated 4 months ago
- SenePy is a set of tools to score single-cells based on their expression of cell-specific senescence markers. Please see the following pu…☆44Updated 8 months ago