55 dependents
| Package | Description | Downloads/month |
|---|---|---|
| Build contrasts for models defined with formulaic | 512K | |
| Spatial hotspot analysis | 433K | |
| Ordered Niche Trajectory Construction | 5K | |
| Mapping Vector Field of Single Cells | 4K | |
| Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.... | 3K | |
| The balance python package offers a simple workflow and methods for dealing with... | 3K | |
| A Python alternative to `clustree` for assessing single-cell RNA-sequencing clus... | 2K | |
| Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data | 2K | |
| A Python package for the identification, characterization and comparison of spat... | 2K | |
| cnvturbo: A high-performance scRNA-seq CNV inference toolkit with R inferCNV-com... | 1K | |
| Run Gaussian Mixture Models on single or multiple CPUs/GPUs | 1K | |
| Allows generating dummy anndata objects, useful for testing. | 1K | |
| The single T cell annotation tool for scRNA-seq data | 1K | |
| Run_dbcan V5 | 1K | |
| sequence | 1K | |
| Analyze cellular niches in single-cell spatial transcriptomics data | 946 | |
| Modeling complex perturbations with CellFlow | 808 | |
| a simpler version of flashattention | 784 | |
| Geometric Learning for Genome Data | 715 | |
| Data preprocessing for bolero package | 648 | |
| A GUI for (imaging) mass cyometry analysis predominantly based on the popular St... | 644 | |
| A deep generative framework for disentangling known and unknown attributes in si... | 478 | |
| A model for classification of cells into marker positive / negative | 477 | |
| Aligned Cross-modal Integration and Characterization of Single-Cell Multiomic Da... | 449 | |
| A Python implementation of the LEMUR algorithm for analyzing multi-condition sin... | 444 | |
| ChromBPNet pytorch | 350 | |
| KAILINss - TOGGLE(KAILIN): Single Cell Fate Tracing tools | 333 | |
| Feature Clock: High-Dimensional Effects in Two-Dimensional Plots | 306 | |
| KAILINss - TOGGLE(KAILIN): Single Cell Fate Tracing tools | 296 | |
| Multimodal weakly supervised learning to identify disease-specific changes in si... | 295 | |
| Run_dbcan V5 | 287 | |
| BEASTsim (BEnchmarking and Analysis of Spatial Transcriptomics simulations) is a... | 287 | |
| Genomic annotations using BioConductor resources in Python. | 256 | |
| A command-line and python toolkit for QC, counting, clustering and plotting of s... | 253 | |
| Modeling whole bacterial genome as a sequence of proteins. | 230 | |
| Single-cell morphological analysis | 226 | |
| scanpy extra function for STOmics | 186 | |
| Bayesian model for RNA velocity estimation of periodic manifolds | 172 | |
| Model your architecture in an easy to understand language inspired by Yaml, and ... | 165 | |
| Sobolev alignment of deep probabilistic models for comparing single cell profile... | 155 | |
| Shared-private Variational Inference with Product of Experts and Supervision | 149 | |
| scverse lineage tracing analysis toolkit | 142 | |
| STDrug: A Computational Method to Use Spatial Transcriptomics to Aid Personalize... | 134 | |
| Optimal gating strategies for flow and mass cytometry. | 134 | |
| A minimal reader for .gef files | 123 | |
| TFs, IEGs and more! | 119 | |
| Cellular decomposition of intrinsic and niche-induced omic effects | 105 | |
| A hyperparameter-randomized ensemble approach for robust clustering across diver... | 105 | |
| Cross-attention-based cell-cell interaction inference from ST data. | 99 | |
| Evaluation metrics for scvi-tools models | 85 |
