Reverse Dependencies of squidpy

The following projects have a declared dependency on squidpy:

• aestetik — AESTETIK: AutoEncoder for Spatial Transcriptomics Expression with Topology and Image Knowledge
• ai4scr-athena — ATHENA package provides methods to analyse spatial heterogeneity in spatial omics data
• B-HIT — A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
• campa — no summary
• cellcharter — A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
• celldega — no summary
• citegeist — A spatial transcriptomics deconvolution tool for cell type identification and gene expression analysis
• DeepTalk-ST — Cell-cell communication prediction for ST data
• entrain — A single-cell analysis package to elucidate environmental factors controlling cell differentiation in RNA velocity and spatial datasets.
• entrain-spatial — A single-cell analysis package to elucidate environmental factors controlling cell differentiation in spatial datasets.
• eykthyr — Eykthyr: Revealing transcriptional regulators of spatial gene programs
• FineST — FineST: Fine-grained Spatial Transcriptomic
• geome — Geometric Learning for Genome Data
• geospace-st — GeoSpace method for identifying multiscale structure in spatial transcriptomic data
• glue-genes — Multidimensional data visualization for genomics
• graphcompass — Spatial metrics for differential analyses of cell organization across conditions
• graphxl — Workbench for Deep Learning on network datasets
• harpy-analysis — single-cell spatial proteomics analysis that makes you happy
• imc-analysis — A multi-file Python command line tool with commands qc, phenotype, and visualize.
• maxspin — Estimate spatial information in spatial -omics datasets.
• metachat — Spatial metabolic communication flow of single cells.
• metaspace-converter — Convert Metaspace datasets to AnnData
• MILWRM — Multiplex Image Labeling With Regional Morphology
• moscot — Multi-omic single-cell optimal transport tools
• napari-prism — A Python package for the inteRactive and Integrated analySis of Multiplexed tissue microarrays
• napari-spatialdata — Interactive visualization of spatial omics data with napari
• ncem — ncem. Learning cell communication from spatial graphs of cells.
• nichecompass — End-to-end analysis of spatial multi-omics data
• nichejepa — Spatial omics foundation model
• palmettobug — A GUI for (imaging) mass cyometry analysis predominantly based on the popular Steinbock and CATALYST image processing and data analysis packages and written in customtkinter.
• panpipes — Panpipes - multimodal single cell pipelines
• plastinet — Plastinet is Python package for spatial transcriptomics.
• popari — Popari: a probabilistic graphical model for integrated spatial transcriptomics analysis
• process-hdst — Downstream analysis tool for spatial transcriptomics data, especially for data from HDSTDb
• scCellFie — A tool for inferring metabolic activities from single-cell and spatial transcriptomics
• scTM — A toolbox for single cell topic models
• sctriangulate — A Python package to mix-and-match conflicting clustering results in single cell analysis, and generate reconciled clustering solutions.
• scvi-tools — Deep probabilistic analysis of single-cell omics data.
• SEAGAL — Spatial Enrichment Analysis of Gene Association using L-index
• seu3d-tool — A web server for visualization of spatial-temporal single cell transcriptomics data
• SOMENDER — TBD
• space-srt — SPatial transcriptomics Analysis via Cell Embedding
• SpaceFlow — Identifying Spatiotemporal Patterns of Cells for Spatial Transcriptome Data
• SPACEL — SPACEL: characterizing spatial transcriptome architectures by deep-learning
• spatial-aging-clock — Spatial Aging Clock
• spatial-analysis-toolkit — tools for interacting with spatial data
• spatial-eggplant — Landmark-based transfer of spatial transcriptomics data
• spatial-utils — a collection of utilities for spatial-omics analysis
• spatialleiden — Implementation of multiplex Leiden for analysis of spatial omics data.
• spatialprofilingtoolbox — Toolbox for spatial analysis of single cell data.
• spicemix — SpiceMix: a probabilistic graphical model for spatial transcriptomics data
• spider-st — Identifying spatially variable interactions
• spiderYa — Identifying spatially variable interactions
• spotiphy — An integrated pipeline designed to deconvolute and decompose spatial transcriptomics data, and produce pseudo single-cell resolution images.
• SpottedPy — Spatial hotspot analysis
• st-graphpca — A fast and interpretable dimension reduction algorithm for spatial transcriptomics data.
• st-spider — A tools to simulate spatial transcriptomics data.
• stars-omics — A spatial transcriptomics analysis tool.
• StereoUtils — scanpy extra function for STOmics
• STHD — STHD: probabilistic cell typing of single Spots in whole Transcriptome spatial data with High Definition
• tissue-sc — TISSUE (Transcript Imputation with Spatial Single-cell Uncertainty Estimation) provides tools for estimating well-calibrated uncertainty measures for gene expression predictions in single-cell spatial transcriptomics datasets and utilizing them in downstream analyses
• transpa — Translation-based imputation and cell type deconvolution
• xclone — Inference of clonal Copy Number Alterations in single cells