849 dependents
| Package | Description | Downloads/month |
|---|---|---|
| Single-cell analysis in Python. Scales to >100M cells. | 815K | |
| Spatially-aware quality control for spatial transcriptomics | 539K | |
| A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA. | 532K | |
| Spatial hotspot analysis | 433K | |
| Multimodal Data (.h5mu) implementation for Python | 147K | |
| An open and interoperable data framework for spatial omics data | 105K | |
| This API provides programmatic access to the AlphaGenome model developed by Goog... | 89K | |
| 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 | |
| A flexible and extensible API for annotated 2D matrix data stored in multiple un... | 62K | |
| CREsted is a Python package for training sequence-based deep learning models on ... | 62K | |
| CZ CELLxGENE Discover Census | 55K | |
| Python package to perform enrichment analysis from omics data. | 49K | |
| Spatial Single Cell Analysis in Python | 43K | |
| A user-friendly library that brings familiar DataFrame-style operations to AnnDa... | 39K | |
| Fast asymptotic mannwhitney-u test | 34K | |
| Read fcs files. | 28K | |
| 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 | |
| Convert between AnnData and SingleCellExperiment | 25K | |
| Accelerated, Python-only, single-cell integration benchmarking metrics | 22K | |
| Benchmarking analysis of data integration tools | 18K | |
| RNA Velocity generalized through dynamical modeling | 18K | |
| 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 | |
| Out-of-memory AnnData powered by Rust — a drop-in replacement for anndata.AnnDat... | 11K | |
| A framework that allows processing of multi-modal single-cell data | 11K | |
| Parallel differential expression for single-cell perturbation sequencing | 10K | |
| CellRank: dynamics from multi-view single-cell data | 9K | |
| ngio is a Python library to streamline OME-Zarr image analysis workflows. | 8K | |
| 8K | ||
| Python interface to TileDB Cloud REST API | 8K | |
| A Python implementation of the M3Drop single-cell RNA-seq analysis tool. | 7K | |
| Identifying recurrent gene programs in single-cell sequencing data | 7K | |
| Gene regulatory network inference | 7K | |
| PyWGCNA is a Python package designed to do Weighted Gene Correlation Network ana... | 7K | |
| rapids-singlecell: GPU-accelerated framework for scRNA analysis | 7K | |
| Single-cell epigenomics analysis tools | 7K | |
| A framework for state-of-the-art pre-trained bio foundation models on genomics a... | 7K | |
| A scanpy extension to analyse single-cell TCR and BCR data. | 6K | |
| Single cell trajectory detection | 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 | |
| Evaluation metrics for single-cell perturbation predictions | 5K | |
| A toolkit for processing single cell Hi-C data | 5K |
