estellad / SpatialExperimentIO
Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
☆10Updated last month
Alternatives and similar repositories for SpatialExperimentIO:
Users that are interested in SpatialExperimentIO are comparing it to the libraries listed below
- ☆12Updated 10 months ago
- A repository for benchmarking spatial deconvolution and mapping tools☆33Updated 2 months ago
- ☆25Updated 5 months ago
- An R package for handling and analysing imaging mass cytometry data☆24Updated 5 months ago
- Cell type pipes for R☆51Updated last year
- R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)☆9Updated last year
- CAST package☆32Updated 5 months ago
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆31Updated 9 months ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆14Updated 3 years ago
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆17Updated 5 months ago
- A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.☆24Updated 2 months ago
- Python package for Probe set selection for targeted spatial transcriptomics.☆35Updated 4 months ago
- Quasilinear data representations for single-cell omics data analysis☆42Updated last year
- Interoperability between SpatialData and the Xenium Explorer☆20Updated 8 months ago
- Identification of spatial homogeneous regions☆20Updated 2 months ago
- ☆21Updated 2 years ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆69Updated 2 years ago
- Using self-organizing maps for visualization and interpretation of cytometry data☆27Updated 2 weeks ago
- Multi-resolution Variational Inference☆22Updated 3 weeks ago
- AnnData interoperability in R☆72Updated 2 weeks ago
- Segmentation error aware clustering for multiplexed imaging☆15Updated 2 months ago
- Stitch multiple Visium slides together☆15Updated last year
- Probabilistic cell segmentation for in situ spatial transcriptomics☆67Updated this week
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆51Updated 3 weeks ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆26Updated 3 weeks ago
- ☆40Updated 3 years ago
- Mosaic single cell data integration using non-overlapping features☆37Updated 2 years ago
- Flexible, probablistic metrics for quality control of scRNA-seq data☆19Updated 2 years ago
- ☆33Updated last year
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆33Updated 2 weeks ago