45 dependents
| Package | Description | Downloads/month |
|---|---|---|
| SCIV algorithm | 11K | |
| Python package for systematic assessment of clustering results stability on sing... | 11K | |
| A framework for state-of-the-art pre-trained bio foundation models on genomics a... | 7K | |
| 实现一些数学计算工具的 MCP Server | 5K | |
| This is the alpha version of the CellOracle package | 3K | |
| Popari: a probabilistic graphical model for integrated spatial transcriptomics a... | 3K | |
| A toolkit of spatial transcriptomic analysis. | 2K | |
| MultiGATE single cell | 2K | |
| STACCI for STCase | 2K | |
| A single-cell analysis pipeline. | 2K | |
| SMODER: spatial multi-omics deconvolution toolkit | 1K | |
| SPatial Analysis for CodEX data (SPACEc) | 1K | |
| Scripts for using scanpy | 1K | |
| spatial tools for S1000 | 839 | |
| Single-Cell Clustering Assessment Framework | 837 | |
| Python package for integrating and analyzing multiple single-cell datasets (A Py... | 813 | |
| Package for paper: Optimal transport modeling uncovers spatial domain dynamics i... | 581 | |
| A package for automatic clustering hyperparameter optmization | 516 | |
| SpaGFT: Graph Fourier transform for spatial omics representation and analyses of... | 516 | |
| Single-cell data analysis | 504 | |
| Morphology-Enhanced Spatial Transcriptome Analysis Integrator | 465 | |
| Panpipes - multimodal single cell pipelines | 396 | |
| stClinic for dissecting clinically relevant niches by integrating spatial multi-... | 385 | |
| Evolutionary velocity with protein language models | 320 | |
| 270 | ||
| Identification of spatial domains in spatial transcriptomics by deep learning. | 269 | |
| scE2TM improves single-cell embedding interpretability and reveals cellular pert... | 259 | |
| Cross-modality representation and multi-sample integration of spatially resolved... | 254 | |
| ncem. Learning cell communication from spatial graphs of cells. | 253 | |
| Backend library for conversational AI in biomedicine | 245 | |
| Comprehensive spatial transcriptomics analysis library with advanced segmentatio... | 237 | |
| Spatial Transcriptomics cell-cell Communication and subtype exploration | 200 | |
| A pipeline for mapping scRNA-seq query cells to reference cell states using Hots... | 198 | |
| SpaCon: integrative analysis of spatial transcriptome and connectome | 178 | |
| A Python package for modeling cell–cell communication using reaction-diffusion a... | 146 | |
| Single-cell RNA sequencing data excels in providing high sequencing depth and pr... | 143 | |
| scConfluence is a novel diagonal integration method combining uncoupled autoenco... | 139 | |
| An efficient, accurate and flexible method for single-cell data integration. | 135 | |
| STDrug: A Computational Method to Use Spatial Transcriptomics to Aid Personalize... | 134 | |
| A toolkit package of data integration | 114 | |
| qytoolspkg is a package for data processing and data analysis. | 114 | |
| Eykthyr: Revealing transcriptional regulators of spatial gene programs | 110 | |
| SIMO: Spatial Integration of Multi-Omics single-cell datasets through probabilis... | 69 | |
| extract orthologous maps (short: orthomap) from OrthoFinder output for query spe... | 57 | |
| SCOTCH is a Single-Cell multi-modal integration method leveraging the Optimal Tr... | 28 |
