chanzuckerberg / single-cell-curation
Code and documentation for the curation of cellxgene datasets
☆44Updated this week
Alternatives and similar repositories for single-cell-curation:
Users that are interested in single-cell-curation are comparing it to the libraries listed below
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆52Updated 8 months ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆71Updated 3 months ago
- Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…☆63Updated last year
- Geometry-preserving random sampling☆81Updated 6 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆68Updated 2 months ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated last year
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆110Updated last year
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆41Updated last year
- Single-Cell Clustering Assessment Framework☆101Updated last year
- Single cell omics biology annotations☆51Updated 2 weeks ago
- ☆35Updated 2 months ago
- ☆53Updated last month
- Quasilinear data representations for single-cell omics data analysis☆42Updated 2 years ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆68Updated 3 weeks ago
- ☆43Updated 3 weeks ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆73Updated last month
- ☆40Updated 5 months ago
- ☆42Updated 6 months ago
- Convert between AnnData and SingleCellExperiment☆132Updated last week
- ☆46Updated 2 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 10 months ago
- ☆59Updated 3 years ago
- Imputation method for scRNA-seq based on low-rank approximation☆74Updated last year
- Multimodal Data (.h5mu) implementation for Python☆95Updated last month
- Gene group activity utility functions for Scanpy☆74Updated 4 months ago
- A repository of pipelines for single-cell data in Nextflow DSL2☆75Updated 2 years ago
- All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs☆41Updated 2 years ago
- A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…☆61Updated last month
- software to detect doublets☆92Updated 4 months ago
- R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.☆45Updated 4 months ago