cantinilab / Circe
Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).
☆21Updated 2 weeks ago
Alternatives and similar repositories for Circe:
Users that are interested in Circe are comparing it to the libraries listed below
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆40Updated 3 months ago
- Single cell omics biology annotations☆51Updated 2 weeks ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆68Updated 3 weeks ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated last year
- ☆50Updated 7 months ago
- ☆35Updated 8 months ago
- PhyloVelo, Phylogeny-based transcriptomic velocity of single cells☆43Updated last year
- Multi-resolution Variational Inference☆22Updated last month
- Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics☆46Updated 2 weeks ago
- R implementation of GeneTrajectory☆58Updated last year
- Python implementation of Milo for differential abundance testing on KNN graph☆68Updated 2 months ago
- Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020☆16Updated last year
- A python package for chromVAR☆27Updated 2 years ago
- Python implementation of Gene Trajectory☆25Updated 8 months ago
- ☆43Updated last year
- inferring regulatory cellular dynamics☆41Updated this week
- Pipeline to run scE2G☆24Updated last week
- Functional Inference of Gene Regulation☆43Updated 10 months ago
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆28Updated 5 months ago
- Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq☆13Updated last year
- ☆38Updated 2 weeks ago
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆41Updated last year
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 10 months ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆73Updated last month
- Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition☆58Updated last year
- A set of files to do genomics analysis on python☆18Updated 5 months ago
- Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases☆31Updated 2 weeks ago
- Parse ArchR arrow files to anndata h5ad☆13Updated last year
- ☆26Updated last year