Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
Top 3.2% on pypi.org
Top 3.9% downloads on pypi.org
Top 0.4% dependent packages on pypi.org
Top 3.0% dependent repos on pypi.org
Top 5.4% forks on pypi.org
Top 3.2% docker downloads on pypi.org
Top 3.9% downloads on pypi.org
Top 0.4% dependent packages on pypi.org
Top 3.0% dependent repos on pypi.org
Top 5.4% forks on pypi.org
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pypi.org : squidpy
Spatial Single Cell Analysis in Python
Registry
-
Source
- Documentation
- JSON
purl: pkg:pypi/squidpy
Keywords: bio-informatics, image analysis, single-cell, spatial data analysis, spatial transcriptomics, data-visualization, image-analysis, single-cell-genomics, single-cell-rna-seq, spatial-analysis, spatial-transcriptomics, squidpy
License: Other
Latest release: 4 months ago
First release: over 3 years ago
Dependent packages: 43
Dependent repositories: 23
Downloads: 6,664 last month
Stars: 397 on GitHub
Forks: 71 on GitHub
Docker dependents: 5
Docker downloads: 990
Total Commits: 514
Committers: 37
Average commits per author: 13.892
Development Distribution Score (DDS): 0.745
More commit stats: commits.ecosyste.ms
See more repository details: repos.ecosyste.ms
Last synced: 13 days ago
pseudovisium 0.0.23
Python package for hexagonal binning of high-resolution spatial transcriptomic data39 versions - Latest release: 24 days ago - 1.39 thousand downloads last month - 1 maintainer
spatialprofilingtoolbox 0.23.3
Toolbox for spatial analysis of single cell data.90 versions - Latest release: 24 days ago - 1 dependent package - 1 dependent repositories - 269 downloads last month - 22 stars on GitHub - 1 maintainer
mnsf 0.1.3
multi-sample non-negative spatial factorization5 versions - Latest release: 29 days ago - 213 downloads last month - 1 maintainer
sccellfie 0.1.11
A tool for studying metabolic tasks from single-cell and spatial transcriptomics13 versions - Latest release: about 1 month ago - 334 downloads last month - 1 maintainer
panpipes 0.5.0
Panpipes - multimodal single cell pipelines7 versions - Latest release: about 1 month ago - 27 downloads last month - 36 stars on GitHub - 2 maintainers
sctm 0.1.3
A toolbox for single cell topic models3 versions - Latest release: about 1 month ago - 24 downloads last month - 0 stars on GitHub - 1 maintainer
nichejepa 0.0.0
Spatial omics foundation model1 version - Latest release: about 2 months ago - 168 downloads last month - 1 maintainer
spotiphy 0.1.3
An integrated pipeline designed to deconvolute and decompose spatial transcriptomics data, and pr...4 versions - Latest release: about 2 months ago - 36 downloads last month - 1 stars on GitHub - 1 maintainer
liana 1.1.0
LIANA+: a one-stop-shop framework for cell-cell communication18 versions - Latest release: about 2 months ago - 1.79 thousand downloads last month - 120 stars on GitHub - 1 maintainer
st-graphpca 0.1.3
A fast and interpretable dimension reduction algorithm for spatial transcriptomics data.13 versions - Latest release: 2 months ago - 136 downloads last month - 1 stars on GitHub - 1 maintainer
napari-spatialdata 0.4.1
Interactive visualization of spatial omics data with napari14 versions - Latest release: 2 months ago - 1 dependent package - 756 downloads last month - 33 stars on GitHub - 1 maintainer
Top 9.0% on pypi.org
29 versions - Latest release: 2 months ago - 1 dependent repositories - 1.12 thousand downloads last month - 171 stars on GitHub - 1 maintainer
stereopy 1.2.0
Spatial transcriptomic analysis in python.29 versions - Latest release: 2 months ago - 1 dependent repositories - 1.12 thousand downloads last month - 171 stars on GitHub - 1 maintainer
metaspace-converter 1.1.1
Convert Metaspace datasets to AnnData4 versions - Latest release: 3 months ago - 40 downloads last month - 7 stars on GitHub - 1 maintainer
moscot 0.3.4
Multi-omic single-cell optimal transport tools7 versions - Latest release: 3 months ago - 215 downloads last month - 96 stars on GitHub - 1 maintainer
stereosite 1.1.5
Analysis spatial transcriptomics data13 versions - Latest release: 3 months ago - 96 downloads last month - 18 stars on GitHub - 1 maintainer
tissue-sc 1.0.1
TISSUE (Transcript Imputation with Spatial Single-cell Uncertainty Estimation) provides tools for...4 versions - Latest release: 3 months ago - 62 downloads last month - 22 stars on GitHub - 1 maintainer
graphcompass 0.2.2
Spatial metrics for differential analyses of cell organization across conditions7 versions - Latest release: 3 months ago - 56 downloads last month - 15 stars on GitHub - 2 maintainers
Top 1.9% on pypi.org
77 versions - Latest release: 3 months ago - 43 dependent packages - 41 dependent repositories - 20.5 thousand downloads last month - 1,113 stars on GitHub - 3 maintainers
scvi-tools 1.1.2
Deep probabilistic analysis of single-cell omics data.77 versions - Latest release: 3 months ago - 43 dependent packages - 41 dependent repositories - 20.5 thousand downloads last month - 1,113 stars on GitHub - 3 maintainers
graphxl 0.1.0
Workbench for Deep Learning on network datasets2 versions - Latest release: 3 months ago - 8 downloads last month - 32 stars on GitHub - 1 maintainer
st-spider 0.2.5
A tools to simulate spatial transcriptomics data.25 versions - Latest release: 4 months ago - 183 downloads last month - 1 stars on GitHub - 1 maintainer
nichecompass 0.1.2
End-to-end analysis of spatial multi-omics data3 versions - Latest release: 4 months ago - 52 downloads last month - 24 stars on GitHub - 1 maintainer
popari 0.0.72
Popari: a probabilistic graphical model for integrated spatial transcriptomics analysis67 versions - Latest release: 5 months ago - 416 downloads last month - 3 stars on GitHub - 1 maintainer
pianno 1.0.5
Pattern Image ANNOtation4 versions - Latest release: 5 months ago - 15 downloads last month - 1 maintainer
spacel 1.1.7
SPACEL: characterizing spatial transcriptome architectures by deep-learning11 versions - Latest release: 5 months ago - 83 downloads last month - 34 stars on GitHub - 1 maintainer
stereoutils 0.0.1
scanpy extra function for STOmics1 version - Latest release: 6 months ago - 11 downloads last month - 1 stars on GitHub - 1 maintainer
glue-genes 1.2.2
Multidimensional data visualization for genomics7 versions - Latest release: 7 months ago - 46 downloads last month - 7 stars on GitHub - 1 maintainer
deeptalk-st 0.0.12
Cell-cell communication prediction for ST data3 versions - Latest release: 7 months ago - 21 downloads last month - 0 stars on GitHub - 1 maintainer
somender 1.0.1
TBD3 versions - Latest release: 7 months ago - 13 downloads last month - 4 stars on GitHub - 1 maintainer
seagal 2.5.2
Spatial Enrichment Analysis of Gene Association using L-index32 versions - Latest release: 7 months ago - 296 downloads last month - 3 stars on GitHub - 2 maintainers
entrain 0.0.79
A single-cell analysis package to elucidate environmental factors controlling cell differentiatio...16 versions - Latest release: 8 months ago - 75 downloads last month - 1 maintainer
space-srt 0.6.9
SPatial transcriptomics Analysis via Cell Embedding15 versions - Latest release: 8 months ago - 402 downloads last month - 2 stars on GitHub - 1 maintainer
nest-analysis 1.0.4
NeST method for identifying nested structure in spatial transcriptomic data5 versions - Latest release: 9 months ago - 34 downloads last month - 1 maintainer
spider-st 0.1.45
Identifying spatially variable interactions44 versions - Latest release: 9 months ago - 79 downloads last month - 0 stars on GitHub - 1 maintainer
cellcharter 0.2.0
A Python package for the identification, characterization and comparison of spatial clusters from...6 versions - Latest release: 10 months ago - 296 downloads last month - 68 stars on GitHub - 1 maintainer
sctriangulate 0.13.0
A Python package to mix-and-match conflicting clustering results in single cell analysis, and gen...6 versions - Latest release: 11 months ago - 1 dependent repositories - 246 downloads last month - 27 stars on GitHub - 1 maintainer
transpa 0.1.1
Translation-based imputation and cell type deconvolution1 version - Latest release: 11 months ago - 1 dependent repositories - 26 downloads last month - 3 stars on GitHub - 1 maintainer
geome 0.0.2
Geometric Learning for Genome Data2 versions - Latest release: 12 months ago - 2 dependent repositories - 22 downloads last month - 16 stars on GitHub - 3 maintainers
ncem 0.1.5
ncem. Learning cell communication from spatial graphs of cells.6 versions - Latest release: 12 months ago - 1 dependent repositories - 82 downloads last month - 96 stars on GitHub - 1 maintainer
entrain-spatial 0.0.1
A single-cell analysis package to elucidate environmental factors controlling cell differentiatio...1 version - Latest release: 12 months ago - 8 downloads last month - 1 maintainer
milwrm 1.1.1
Multiplex Image Labeling With Regional Morphology19 versions - Latest release: about 1 year ago - 1 dependent repositories - 119 downloads last month - 1 stars on GitHub - 2 maintainers
Top 9.8% on pypi.org
23 versions - Latest release: about 1 year ago - 111 downloads last month - 0 stars on GitHub - 2 maintainers
spiderya 0.1.7
Identifying spatially variable interactions23 versions - Latest release: about 1 year ago - 111 downloads last month - 0 stars on GitHub - 2 maintainers
maxspin 0.1.1
Estimate spatial information in spatial -omics datasets.2 versions - Latest release: about 1 year ago - 15 downloads last month - 5 stars on GitHub - 1 maintainer
campa 1.1.0
Conditional Autoencoders for Multiplexed Pixel Analysis2 versions - Latest release: over 1 year ago - 1 dependent repositories - 10 downloads last month - 13 stars on GitHub - 1 maintainer