pypi.org "spatial-transcriptomics" keyword
View the packages on the pypi.org package registry that are tagged with the "spatial-transcriptomics" keyword.
oligo-designer-toolsuite 1.0.1
Develop custom oligo design pipelines.7 versions - Latest release: 6 months ago - 1 dependent package - 38 downloads last month - 22 stars on GitHub - 3 maintainers
effidict 0.1.1
Fast Python package providing enhanced dictionary-like data structures with advanced caching capa...11 versions - Latest release: 1 day ago - 740 downloads last month - 22 stars on GitHub - 1 maintainer
cell-decipher 0.2.0
Spatial-omics data embedding and analysis3 versions - Latest release: 2 months ago - 107 downloads last month - 22 stars on GitHub - 1 maintainer
sdeper 1.6.4
Spatial Deconvolution method with Platform Effect Removal16 versions - Latest release: 3 months ago - 40 downloads last month - 4 stars on GitHub - 1 maintainer
inigen 0.0.1
Intrinsic and neighborhood-induced gene expression generation1 version - Latest release: 6 months ago - 6 downloads last month - 2 stars on GitHub - 1 maintainer
scslat 0.3.0
A graph deep learning based tool to align single cell spatial omics data3 versions - Latest release: 9 months ago - 106 downloads last month - 87 stars on GitHub - 1 maintainer
sopa 2.1.3
Spatial-omics pipeline and analysis36 versions - Latest release: 15 days ago - 1.46 thousand downloads last month - 218 stars on GitHub - 1 maintainer
pydance 1.0.1
Deep Learning for Single-cell Analysis4 versions - Latest release: almost 2 years ago - 1 dependent package - 1 dependent repositories - 93 downloads last month - 376 stars on GitHub - 2 maintainers
azimuthpy 0.1.1
Python wrapper for Azimuth (Seurat-based single-cell mapping) using rpy22 versions - Latest release: 5 months ago - 38 downloads last month - 1 stars on GitHub - 1 maintainer
holonet 0.1.0
Decoding functional cell–cell communication events by multi-view graph learning on spatial transc...6 versions - Latest release: over 2 years ago - 1 dependent repositories - 26 downloads last month - 20 stars on GitHub - 1 maintainer
pciseq 0.0.61
Probabilistic cell typing for spatial transcriptomics62 versions - Latest release: over 1 year ago - 1 dependent repositories - 156 downloads last month - 24 stars on GitHub - 1 maintainer
elastic-st 0.1.1
A python data science library to build and analyze biological networks from spatial transcriptomi...1 version - Latest release: 9 months ago - 5 downloads last month - 2 stars on GitHub - 1 maintainer
teslaforst 1.2.2
TESLA: Deciphering tumor ecosystems at super-resolution from spatial transcriptomics5 versions - Latest release: over 3 years ago - 1 dependent repositories - 43 downloads last month - 59 stars on GitHub - 1 maintainer
celllens 0.1.1
A package for enhancing single-cell population delineation by integrating cross-domain information.2 versions - Latest release: 4 months ago - 49 downloads last month - 27 stars on GitHub - 1 maintainer
ccsf 1.0.8
Leveraging cell-cell similarity from gene expression data for high-performance spatial and tempor...6 versions - Latest release: about 2 years ago - 29 downloads last month - 1 stars on GitHub - 1 maintainer
mintflow 0.2.0
Microenvironment-induced and INtrinsic Transcriptomic FLOWs3 versions - Latest release: about 2 months ago - 36 downloads last month - 13 stars on GitHub - 2 maintainers
omero-vitessce 1.2.4
OMERO Vitessce multimodal data viewer plugin for OMERO.web20 versions - Latest release: 7 months ago - 29 downloads last month - 10 stars on GitHub - 1 maintainer
stminer 1.1.2
Python package for spatial transcriptomics data analysis15 versions - Latest release: 16 days ago - 143 downloads last month - 15 stars on GitHub - 1 maintainer
heartmap 1.0.2
Heart Multi-chamber Analysis Platform for single-cell RNA-seq2 versions - Latest release: about 1 month ago - 565 downloads last month - 1 stars on GitHub - 1 maintainer
cosg 1.0.3
Accurate and fast cell marker gene identification with COSG3 versions - Latest release: 6 months ago - 2 dependent packages - 1 dependent repositories - 236 downloads last month - 45 stars on GitHub - 1 maintainer
pathml 3.0.2
Tools for computational pathology19 versions - Latest release: 4 months ago - 1 dependent repositories - 203 downloads last month - 435 stars on GitHub - 3 maintainers
enrichmap 0.1.9
EnrichMap: Spatially informed enrichment analysis for functional interpretation of spatial transc...6 versions - Latest release: 3 months ago - 38 downloads last month - 6 stars on GitHub - 1 maintainer
spatialcorr 1.2.0
SpatialCorr3 versions - Latest release: over 2 years ago - 1 dependent repositories - 29 downloads last month - 17 stars on GitHub - 2 maintainers
bellavista 0.0.2
Python package for interactive visualization of imaging-based spatial transcriptomics.2 versions - Latest release: 12 months ago - 19 downloads last month - 5 stars on GitHub - 1 maintainer
sdevelo 0.2.12
SDEvelo: multivariate stochastic modeling for transcriptional dynamics with cell-specific latent ...14 versions - Latest release: 10 months ago - 43 downloads last month - 17 stars on GitHub - 1 maintainer
sccellfie 0.5.0
A tool for inferring metabolic activities from single-cell and spatial transcriptomics29 versions - Latest release: 10 days ago - 139 downloads last month - 36 stars on GitHub - 1 maintainer
xclone 0.3.8
Inference of clonal Copy Number Alterations in single cells9 versions - Latest release: about 1 year ago - 2 dependent repositories - 36 downloads last month - 37 stars on GitHub - 1 maintainer
gps-mapping 1.0.2
Genetics-informed pathogenic spatial mapping7 versions - Latest release: over 1 year ago - 16 downloads last month - 170 stars on GitHub - 1 maintainer
spateo-release 1.1.1
Spatiotemporal modeling of molecular holograms5 versions - Latest release: 6 months ago - 1 dependent package - 1 dependent repositories - 239 downloads last month - 310 stars on GitHub - 2 maintainers
Top 3.2% on pypi.org
20 versions - Latest release: 6 months ago - 43 dependent packages - 23 dependent repositories - 15.2 thousand downloads last month - 506 stars on GitHub - 3 maintainers
squidpy 1.6.5
Spatial Single Cell Analysis in Python20 versions - Latest release: 6 months ago - 43 dependent packages - 23 dependent repositories - 15.2 thousand downloads last month - 506 stars on GitHub - 3 maintainers
aestetik 0.1.0
AESTETIK: AutoEncoder for Spatial Transcriptomics Expression with Topology and Image Knowledge3 versions - Latest release: 12 days ago - 28 downloads last month - 14 stars on GitHub - 1 maintainer
muse-sc 0.0.8
MUSE is a deep learning approach characterizing tissue composition through combined analysis of m...8 versions - Latest release: about 5 years ago - 1 dependent repositories - 38 downloads last month - 35 stars on GitHub - 1 maintainer
comseg 1.8.5
single cell RNA profiling analysis of imaging-based spatial transcriptomics data24 versions - Latest release: 7 months ago - 151 downloads last month - 191 stars on GitHub - 1 maintainer
spatialcell 1.1.1
Integrated pipeline for spatial transcriptomics cell segmentation and annotation using QuPath, Bi...35 versions - Latest release: about 2 months ago - 236 downloads last month - 5 stars on GitHub - 1 maintainer
cellproportion 1.1.0
Cell type proportion analysis for single-cell and spatial transcriptomics data2 versions - Latest release: 15 days ago - 135 downloads last month - 1 maintainer
spahdmap 0.1.4
Interpretable high-definition dimension reduction of spatial transcriptomics data by SpaHDmap13 versions - Latest release: 18 days ago - 148 downloads last month - 10 stars on GitHub - 1 maintainer
Top 6.1% on pypi.org
25 versions - Latest release: about 2 months ago - 11 dependent packages - 2 dependent repositories - 7.09 thousand downloads last month - 152 stars on GitHub - 1 maintainer
decoupler 2.1.1
Python package to perform enrichment analysis from omics data.25 versions - Latest release: about 2 months ago - 11 dependent packages - 2 dependent repositories - 7.09 thousand downloads last month - 152 stars on GitHub - 1 maintainer
scmags 1.7
Single Cell Marker Gene Selection Tool For Spatial Trancriptomics2 versions - Latest release: 12 months ago - 1 dependent repositories - 13 downloads last month - 8 stars on GitHub - 1 maintainer
tumoroscope-pymc 0.1.0
'Tumoroscope' model built with PyMC.1 version - Latest release: almost 3 years ago - 6 downloads last month - 2 stars on GitHub - 1 maintainer
singlecellhaystack 0.0.5
A Python implementation of singleCellHaystack.5 versions - Latest release: about 2 years ago - 29 downloads last month - 12 stars on GitHub - 1 maintainer
napari-sc3d-viewer 1.1.1
A plugin to visualize 3D single cell omics6 versions - Latest release: 3 months ago - 41 downloads last month - 20 stars on GitHub - 1 maintainer
Top 9.8% on pypi.org
7 versions - Latest release: over 2 years ago - 1 dependent repositories - 409 downloads last month - 186 stars on GitHub - 1 maintainer
spagcn 1.2.7
SpaGCN: Integrating gene expression and histology to identify spatial domains and spatially varia...7 versions - Latest release: over 2 years ago - 1 dependent repositories - 409 downloads last month - 186 stars on GitHub - 1 maintainer
spatialdm 0.3.1
SpatialDM: Spatial co-expression Detected by bivariate Moran11 versions - Latest release: about 2 months ago - 1 dependent repositories - 80 downloads last month - 27 stars on GitHub - 2 maintainers
stpipeline 2.0.0
ST Pipeline: An automated pipeline for spatial mapping of unique transcripts17 versions - Latest release: 7 months ago - 2.13 thousand downloads last month - 85 stars on GitHub - 1 maintainer
cellsnap 0.1.0
A package for enhancing single-cell population delineation by integrating cross-domain information.9 versions - Latest release: 12 months ago - 55 downloads last month - 27 stars on GitHub - 1 maintainer
stitch3d 1.0.3
A computational method for tissue 3D reconstruction by joint modeling of multiple spatial transcr...3 versions - Latest release: about 2 years ago - 15 downloads last month - 66 stars on GitHub - 1 maintainer
declust 0.1.8
A cluster-based cell-type deconvolution of spatial transcriptomic data (DECLUST)7 versions - Latest release: 5 months ago - 22 downloads last month - 3 stars on GitHub - 1 maintainer
chrysalis-st 0.2.0
Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datas...3 versions - Latest release: over 1 year ago - 17 downloads last month - 17 stars on GitHub - 1 maintainer
transpa 0.1.1
Translation-based imputation and cell type deconvolution1 version - Latest release: about 2 years ago - 1 dependent repositories - 23 downloads last month - 5 stars on GitHub - 1 maintainer
cytocraft 0.1.12
The Cytocraft package provides prediction of chromosome configuration based on subcellular resolu...23 versions - Latest release: 10 months ago - 32 downloads last month - 0 stars on GitHub - 1 maintainer
openst 0.2.3
The computational pipeline for the Open-ST method.15 versions - Latest release: 10 months ago - 116 downloads last month - 101 stars on GitHub - 2 maintainers
spatialcorr-sim 0.0.1
SpatialCorr2 versions - Latest release: over 3 years ago - 1 dependent repositories - 10 downloads last month - 6 stars on GitHub - 2 maintainers
sthd 1.0.1
STHD: probabilistic cell typing of single Spots in whole Transcriptome spatial data with High Def...2 versions - Latest release: 5 months ago - 24 downloads last month - 20 stars on GitHub - 1 maintainer
splotch-st 1.0.0
Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (S...2 versions - Latest release: 11 months ago - 17 downloads last month - 21 stars on GitHub - 1 maintainer
tumorevo 0.0.1
Simulate and illustrate tumor evolution under different spatial constraints.1 version - Latest release: over 3 years ago - 1 dependent repositories - 5 downloads last month - 6 stars on GitHub - 1 maintainer
cvae-glrm 1.0.5 removed
Conditional Variational AutoEncoder - Graph Laplacian Regularized Model6 versions - Latest release: over 2 years ago - 183 downloads last month - 0 stars on GitHub - 1 maintainer
Related Keywords
bioinformatics
19
single-cell
17
python
10
deep-learning
9
machine-learning
7
transcriptomics
6
single-cell-rna-seq
5
data-science
5
single-cell-analysis
5
spatial-omics
5
spatial transcriptomics
4
computational-biology
4
graph-neural-networks
4
clustering
3
gene-expression
3
graph-convolutional-networks
2
convolutional-neural-networks
2
pytorch
2
deep learning
2
data-visualization
2
visualization
2
napari
2
cell-cell-communication
2
single-cell-genomics
2
image-analysis
2
oligo-design
2
probe-design
2
Spatial transcriptomics
2
cell-type-deconvolution
2
flow-matching
2
cell-segmentation
2
3d-reconstruction
2
spatialdata
2
pipeline
2
multiplexed-imaging
2
spatial-data
2
scRNA-seq
1
genomics
1
proportion-analysis
1
cell-type-analysis
1
data-integration
1
multi-modal-analysis
1
TopAct
1
single-cell-ananlysis
1
tensorflow
1
pipelines
1
cell-annotation
1
QuPath
1
Bin2cell
1
DBiT-seq
1
HDST-seq
1
slide-seq
1
osmFISH
1
MERFISH
1
spatiotemporal
1
bio-informatics
1
image analysis
1
seqFish
1
spatial data analysis
1
Visium
1
stereo-seq
1
statistical-genetics
1
spatial-data-analysis
1
spatial-analysis
1
squidpy
1
single-cell analysis
1
dimension reduction
1
analysis
1
spatial
1
toolkit
1
scrna-seq
1
deconvolution
1
imputation
1
3d-configuration
1
sub-cellular-resolution
1
transcription-center
1
omics
1
machine learning
1
single-cell genomics
1
high-resolution
1
statistical-learning
1
generative-model
1
probabilistic-graphical-models
1
cancer
1
simulation
1
treatment
1
tumor-evolution
1
enrichment
1
enrichment-analysis
1
numba
1
pymc
1
bayesian
1
tumoroscope
1
model
1
bayesian-model
1
hacktoberfest
1
spatial-genomics
1
3d
1
napari-plugin
1
graph-convolutional-network
1