299 dependents
| Package | Description | Downloads/month |
|---|---|---|
| Building a single-cell transcriptome-based coordinate system | 49K | |
| Benchmarking analysis of data integration tools | 18K | |
| A tool for semi-automatic cell type classification | 17K | |
| Analysis tools for single-cell metabolome data. | 15K | |
| exprmat: Routines for expression matrices | 15K | |
| SCIV algorithm | 11K | |
| Python package for systematic assessment of clustering results stability on sing... | 11K | |
| Build and Search a knowledge base for your projects—bringing together code, PDFs... | 9K | |
| Graph-powered code intelligence engine — indexes codebases into a knowledge grap... | 8K | |
| A lite implementation of tfmodisco, a motif discovery algorithm for genomics exp... | 7K | |
| Generative additive model for single cell perturbation v2 | 6K | |
| RISK: a next-generation tool for biological network annotation and visualization | 6K | |
| Learning multi-omics perturbation language | 6K | |
| Automated text analysis with networks | 5K | |
| Agent-first semantic grep — filesystem-native retrieval | 5K | |
| A toolkit for processing single cell Hi-C data | 5K | |
| A tool for analyzing trascriptomes of millions of single cells. | 5K | |
| Opinionated, report-first CLI for single-cell and multi-omics analysis | 5K | |
| Ordered Niche Trajectory Construction | 5K | |
| Large-scale generative pretrain of single cell using transformer. | 4K | |
| Single Cell Analysis Pipelines | 4K | |
| DBRetina Python Package | 4K | |
| trajectory inference | 4K | |
| Mapping Vector Field of Single Cells | 4K | |
| Protein Embedding Model for Structure Search | 4K | |
| Semantic code chunker using Tree-sitter for intelligent code analysis | 4K | |
| A novel machine learning pipeline to analyse spatial transcriptomics data | 3K | |
| Sematic representation learning for single cell perturbation | 3K | |
| A python package for clustering and summarizing graphs of texts. | 3K | |
| Behavioral sequencing and phenotyping with lightweight task specific adaptation | 3K | |
| 3K | ||
| visualize histology images with umap | 3K | |
| Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.... | 3K | |
| dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5'... | 3K | |
| Popari: a probabilistic graphical model for integrated spatial transcriptomics a... | 3K | |
| Embedding methods for structure similarity search | 3K | |
| Analyze and model biomembranes from 3D structural data. | 3K | |
| a scalable python suite for tree inference and advanced pseudotime analysis from... | 2K | |
| Local-first knowledge graph builder with hybrid vector + graph search | 2K | |
| a dataloader to work with large single cell datasets from lamindb | 2K | |
| A Python package using Gromov-Wasserstein distance to compare cell shapes | 2K | |
| Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq ... | 2K | |
| Clustering routines and data structures for entity resolution | 2K | |
| single cell RNA profiling analysis of imaging-based spatial transcriptomics data | 2K | |
| a collection of python scripts and functions for exploratory analysis of bioinfo... | 2K | |
| description | 2K | |
| Integrating transcriptional data to decipher the tumor microenvironment with the... | 2K | |
| A python library for multi omics included bulk, single cell and spatial RNA-seq ... | 2K | |
| A Python Library for Continuous Attractor Neural Networks | 2K | |
| Post-processing tools for aliby pipeline. | 2K |
