Pixie pipeline described in Liu et al., Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering
☆12Aug 3, 2023Updated 2 years ago
Alternatives and similar repositories for pixie
Users that are interested in pixie are comparing it to the libraries listed below
Sorting:
- Python bindings for SingleR☆14Jan 6, 2026Updated last month
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆11Mar 3, 2023Updated 2 years ago
- Camiel's scATAC-seq analysis pipeline☆13Apr 15, 2024Updated last year
- ☆13Feb 12, 2026Updated 2 weeks ago
- Access public biological ontologies.☆15Aug 7, 2024Updated last year
- Build contrasts for models defined with formulaic☆12Updated this week
- Shadow objects for AnnData and MuData (experimental)☆11Feb 28, 2025Updated 11 months ago
- R package for computing Association Plots☆17Nov 4, 2024Updated last year
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆34Dec 11, 2025Updated 2 months ago
- A performant scientific image visualization system.☆36Updated this week
- factor models for omics data☆33Updated this week
- Perturbation-response Score (PS) analysis is a method to quantify diverse perturbation responses and discover novel biological insights i…☆17Apr 20, 2024Updated last year
- A python implementation of scran computeSumFactors: normalization by deconvolution for single-cell RNA-sequencing☆34Nov 4, 2023Updated 2 years ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆71Nov 4, 2024Updated last year
- ☆71Jan 18, 2023Updated 3 years ago
- Paired Insertion Counting for snATAC-seq data☆19May 12, 2025Updated 9 months ago
- ☆18Apr 5, 2024Updated last year
- End-to-end model for cell segmentation and classification☆23Jan 13, 2025Updated last year
- Genomic Features in Python from BioConductor's AnnotationHub☆22Feb 16, 2026Updated last week
- A toolking for cell type hierarchies: marker selection & consistent classification☆22Nov 26, 2023Updated 2 years ago
- CellWalkR: An R Package for integrating single-cell and bulk data to resolve regulatory elements☆22Oct 8, 2025Updated 4 months ago
- ☆29Sep 4, 2023Updated 2 years ago
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆58Aug 17, 2024Updated last year
- ☆22Jan 6, 2026Updated last month
- Image Mass Cytometry analysis pipeline☆26Jun 3, 2025Updated 8 months ago
- multimodal whole slide image registration in a graph structure☆100Jul 4, 2024Updated last year
- Interoperability between SpatialData and the Xenium Explorer☆25Jul 31, 2024Updated last year
- ☆59Jan 9, 2026Updated last month
- Spatial Single-Cell Analysis Toolkit☆110Feb 20, 2026Updated last week
- Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications☆64Mar 14, 2024Updated last year
- ☆64May 21, 2025Updated 9 months ago
- Code used to benchmark Xenium☆76Jun 30, 2024Updated last year
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆39Feb 8, 2026Updated 2 weeks ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆118Jan 22, 2024Updated 2 years ago
- ☆33Oct 4, 2024Updated last year
- Probabilistic cell segmentation for in situ spatial transcriptomics☆151Updated this week
- Gene regulatory network inference for RNA velocity and pseudotime data☆28Nov 6, 2025Updated 3 months ago
- Alignment of spatial genomics data using deep Gaussian processes☆31Dec 14, 2022Updated 3 years ago
- Official repository for Characterization of tumor heterogeneity through segmentation-free representation learning on multiplexed imaging …☆14Sep 28, 2025Updated 4 months ago