mossjacob / pyslingshot
Python implementation of the Slingshot pseudotime algorithm
☆59Updated 10 months ago
Alternatives and similar repositories for pyslingshot:
Users that are interested in pyslingshot are comparing it to the libraries listed below
- Python implementation of Milo for differential abundance testing on KNN graph☆63Updated 3 weeks ago
- Single cell omics biology annotations☆50Updated this week
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated 10 months ago
- ☆51Updated last year
- Metacells - Single-cell RNA Sequencing Analysis☆101Updated 5 months ago
- ☆39Updated this week
- Predict RNA velocity through deep learning☆66Updated last year
- Non-parametric density inference for single-cell analysis.☆67Updated this week
- ☆44Updated 10 months ago
- Multi-omic velocity inference☆109Updated 4 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 8 months ago
- Additional code and analysis from the single-cell integration benchmarking project☆58Updated 2 years ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆109Updated last year
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆64Updated this week
- Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).☆19Updated last month
- A python port of the R package SCTransform:☆19Updated 3 years ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆54Updated this week
- Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.☆46Updated last month
- Gene group activity utility functions for Scanpy☆69Updated 2 months ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆68Updated last month
- Molecular interactions inference from single-cell multi-omics data☆22Updated 4 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆155Updated 8 months ago
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆41Updated last year
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆59Updated 6 months ago
- spatial transcriptome, single cell☆67Updated last year
- ☆36Updated 6 months ago
- Cell cycle inference in single-cell RNA-seq☆43Updated last year
- PhyloVelo, Phylogeny-based transcriptomic velocity of single cells☆43Updated last year
- Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.☆48Updated 8 months ago