841 dependents
| Package | Description | Downloads/month |
|---|---|---|
| Spot pseudo-Imager on top of histology | 460K | |
| Spatial hotspot analysis | 433K | |
| Python helpers for G4X. | 430K | |
| Deep probabilistic analysis of single-cell and spatial omics data | 77K | |
| Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell... | 77K | |
| Building a single-cell transcriptome-based coordinate system | 49K | |
| Static plotting for spatialdata | 45K | |
| Spatial Single Cell Analysis in Python | 43K | |
| LIANA+: an all-in-one framework for cell-cell communication | 28K | |
| muon is a multimodal omics Python framework | 28K | |
| SpatialData IO for common techs | 25K | |
| Accelerated, Python-only, single-cell integration benchmarking metrics | 22K | |
| Benchmarking analysis of data integration tools | 18K | |
| RNA Velocity generalized through dynamical modeling | 18K | |
| A tool for semi-automatic cell type classification | 17K | |
| Interactive visualization of spatial omics data | 15K | |
| Analysis tools for single-cell metabolome data. | 15K | |
| Spatial Single-Cell Analysis Toolkit | 15K | |
| exprmat: Routines for expression matrices | 15K | |
| A python library for multi omics included bulk, single cell and spatial RNA-seq ... | 14K | |
| SCIV algorithm | 11K | |
| Python package for systematic assessment of clustering results stability on sing... | 11K | |
| A framework that allows processing of multi-modal single-cell data | 11K | |
| CellRank: dynamics from multi-view single-cell data | 9K | |
| Single-cell perturbation analysis | 7K | |
| Gene regulatory network inference | 7K | |
| rapids-singlecell: GPU-accelerated framework for scRNA analysis | 7K | |
| UCE is a zero-shot foundation model for single-cell gene expression data | 7K | |
| A scanpy extension to analyse single-cell TCR and BCR data. | 6K | |
| Single cell trajectory detection | 6K | |
| Generative additive model for single cell perturbation v2 | 6K | |
| AI Agents for drug discovery, drug development, and other pharmaceutical R&D. | 6K | |
| Technology-invariant pipeline for spatial omics analysis that scales to millions... | 6K | |
| Learning multi-omics perturbation language | 6K | |
| Evaluation metrics for single-cell perturbation predictions | 5K | |
| A toolkit for processing single cell Hi-C data | 5K | |
| STAT: Spatial Transcriptomics Analytical agenT — AI-powered platform for spatial... | 5K | |
| Opinionated, report-first CLI for single-cell and multi-omics analysis | 5K | |
| lib310 Python Package | 4K | |
| Large-scale generative pretrain of single cell using transformer. | 4K | |
| Single Cell Analysis Pipelines | 4K | |
| trajectory inference | 4K | |
| CellPhoneDB can be used to search for a particular ligand/receptor, or interroga... | 4K | |
| A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-proce... | 4K | |
| Single-cell RNA Binding Protein Regulon Inference | 4K | |
| WASP2: High-performance allele-specific analysis pipeline for next-generation se... | 4K | |
| A novel machine learning pipeline to analyse spatial transcriptomics data | 3K | |
| Doublet detection in single-cell RNA-seq data. | 3K | |
| Sematic representation learning for single cell perturbation | 3K | |
| Efficient tool to query spatial pattern of spatial-modalities data | 3K |
