42 dependents
| Package | Description | Downloads/month |
|---|---|---|
| Deep probabilistic analysis of single-cell and spatial omics data | 77K | |
| LIANA+: an all-in-one framework for cell-cell communication | 28K | |
| muon is a multimodal omics Python framework | 28K | |
| exprmat: Routines for expression matrices | 15K | |
| SCIV algorithm | 11K | |
| Single-cell perturbation analysis | 7K | |
| A scanpy extension to analyse single-cell TCR and BCR data. | 6K | |
| The self-evolving agentic framework for bioinformatics | 5K | |
| Mapping Vector Field of Single Cells | 4K | |
| 3K | ||
| Multi-omic single-cell optimal transport tools | 2K | |
| The complete FlowSOM package known from R, now available in Python! | 2K | |
| A torch-based integration method for single-cell multi-omic data. | 2K | |
| factor models for omics data | 927 | |
| Cell-centric ML training backend on LanceDB and sharded zarr | 743 | |
| Comprehensive agentic AI platform for end-to-end cancer research and precision o... | 728 | |
| Python toolkit for LC-MS/MS Proteomics analysis based on MuData | 658 | |
| A GUI for (imaging) mass cyometry analysis predominantly based on the popular St... | 644 | |
| Package to evaluate gene regulatory networks (GRNs). | 542 | |
| SCIV: Unveiling the pivotal cell types involved in variant function regulation a... | 469 | |
| Semi-paired single-cell multimodal integration with Champollion | 430 | |
| Cell-centric ML training backend on LanceDB and sharded zarr | 373 | |
| Salamander is a non-negative matrix factorization framework for signature analys... | 366 | |
| Spatial Multimodal Self-supervised Transformer | 358 | |
| A python package for chromVAR | 352 | |
| MuVI: A multi-view latent variable model with domain-informed structured sparsit... | 336 | |
| TrajAtlas, a trajectory-centric framework reveals differentiation heterogenity a... | 321 | |
| Multimodal datasets, in MuData format | 288 | |
| BEASTsim (BEnchmarking and Analysis of Spatial Transcriptomics simulations) is a... | 287 | |
| Mowgli is a novel method for the integration of paired multi-omics data with any... | 259 | |
| A command-line and python toolkit for QC, counting, clustering and plotting of s... | 253 | |
| Multi-Dimensional Visualization (MDV) is an open-source toolkit for analyzing an... | 232 | |
| Python package designed for single-cell calling cards data | 232 | |
| UniCell Deconvolve - Cloud Cell Type Deconvolution For Transcriptomic Data | 164 | |
| Biologically Guided Variational Inference for Interpretable Multimodal Single-Ce... | 142 | |
| scConfluence is a novel diagonal integration method combining uncoupled autoenco... | 139 | |
| scverse bundle | 131 | |
| Machine learning development environment for single-cell sequencing data analyse... | 120 | |
| multiHIVE, a hierarchical multimodal deep generative model for integrating multi... | 111 | |
| Mapping multi-scale gene regualtion using single-cell multiome | 81 | |
| scMagnify is a versatile Python toolkit for inferring and analyzing gene regulat... | 71 | |
| Chromatin analysis module | 68 |
