dmcable / spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
☆311Updated 5 months ago
Related projects ⓘ
Alternatives and complementary repositories for spacexr
- A package to help convert different single-cell data formats to each other☆382Updated 8 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆297Updated 4 months ago
- A tool for semi-automatic cell type classification☆296Updated 5 months ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆292Updated last month
- NicheNet: predict active ligand-target links between interacting cells☆487Updated 2 months ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆321Updated last month
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆218Updated last year
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆335Updated last month
- Interpretation of cell states using reference single-cell maps☆252Updated this week
- A toolkit of spatial transcriptomic analysis.☆201Updated this week
- This is the alpha version of the CellOracle package☆313Updated this week
- R package for integrating and analyzing multiple single-cell datasets☆390Updated last week
- ☆239Updated last week
- A toolkit for single-cell immune profiling☆310Updated last week
- R package for detecting doublets in single-cell RNA sequencing data☆415Updated 6 months ago
- Analysis of single cell RNA-seq data course☆124Updated 2 years ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆186Updated 2 months ago
- ☆210Updated 4 months ago
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆216Updated this week
- Analysis Pipeline for Single Cell ATAC-seq☆306Updated last year
- Single-cell Transcriptome and Regulome Analysis Pipeline☆279Updated last year
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆274Updated 4 years ago
- EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.☆184Updated 7 months ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆387Updated last week
- Scanpy Tutorials.☆188Updated this week
- Spatial omics analysis toolbox☆265Updated this week
- Single cell RNA sequencing analysis course☆195Updated last month
- ☆345Updated 2 years ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆211Updated 8 months ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆276Updated 2 months ago