63 dependents
| Package | Description | Downloads/month |
|---|---|---|
| exprmat: Routines for expression matrices | 15K | |
| SCIV algorithm | 11K | |
| Large-scale generative pretrain of single cell using transformer. | 4K | |
| Comprehensive mapping of tissue cell architecture via integrated single cell and... | 2K | |
| Compositional Perturbation Autoencoder (CPA) | 2K | |
| CALM-Data-Generator is a comprehensive Python library for synthetic data generat... | 2K | |
| Consensus prediction of cell type labels with popV | 2K | |
| A multivariate RNA Velocity model to estimate future cell states with uncertaint... | 2K | |
| Unsupervised Deep Disentangled Representation of Single-Cell Omics | 1K | |
| 1K | ||
| Single cell perturbation prediction | 866 | |
| Probabilistic modeling of cellular dynamics | 761 | |
| Transfer learning for spatial transcriptomics data and single-cell RNA-seq data. | 742 | |
| Variational Inference for Cell Type Evolution | 710 | |
| UNAGI: deep generative AI for virtual disease and unsuperivsed in-silico perturb... | 627 | |
| CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Tran... | 615 | |
| Graph-based age dependency analysis on scVI latent space with Moran's I, ADI, dC... | 593 | |
| Interpretable Accessibility ODE VAE for scATAC-seq | 581 | |
| Stack is a single-cell foundation model that enables in-context learning at infe... | 521 | |
| Tools for single cell RNA sequencing pipelines | 499 | |
| A deep generative framework for disentangling known and unknown attributes in si... | 478 | |
| SCIV: Unveiling the pivotal cell types involved in variant function regulation a... | 469 | |
| Perturbational analysis by causality-aware generative model for single-cell RNA-... | 463 | |
| Cell DISentangled Experts for Covariate counTerfactuals (CellDISECT). Causal gen... | 452 | |
| Repository for ENACT pipeline for end-to-end analysis of Visium HD data | 444 | |
| Convenient and user-friendly package to streamline common workflows in single-ce... | 404 | |
| Panpipes - multimodal single cell pipelines | 396 | |
| Estimation of RNA velocity with variational inference. | 378 | |
| single cell annotation | 350 | |
| A versatile single-cell cross-modality translation method via dual-aligned varia... | 319 | |
| Tumor-reactivity prediction for single-cell and spatial transcriptomics data. | 316 | |
| Multimodal weakly supervised learning to identify disease-specific changes in si... | 295 | |
| BEASTsim (BEnchmarking and Analysis of Spatial Transcriptomics simulations) is a... | 287 | |
| 272 | ||
| Comprehensive spatial transcriptomics analysis library with advanced segmentatio... | 237 | |
| Exapliner of scANVI using SHAP | 226 | |
| Multi-resolution Variational Inference | 200 | |
| align query dataset to reference atlases. | 192 | |
| 189 | ||
| Multi-modal Disentanglement of Spatial Transcriptomics and Histopathology Imagin... | 178 | |
| Factor Disentanglement Variational Inference for single-cell batch integration w... | 176 | |
| Generation of disentangled microenvironment-induced and intrinsic gene expressio... | 159 | |
| Sobolev alignment of deep probabilistic models for comparing single cell profile... | 155 | |
| Shared-private Variational Inference with Product of Experts and Supervision | 149 | |
| Estimation of RNA velocity with variational inference. | 143 | |
| Revealing the biological utility of gene imputation in spatial transcriptomics | 136 | |
| Lorentz-irecon VAE for Enhancing Single-cell Multi-omics Embeddings | 135 | |
| scDiffusion-X: Diffusion Model for Single-Cell Multiome Data Generation and Anal... | 130 | |
| A toolkit package of data integration | 114 | |
| multiHIVE, a hierarchical multimodal deep generative model for integrating multi... | 111 |
