mossjacob / pyslingshot
Python implementation of the Slingshot pseudotime algorithm
☆51Updated 6 months ago
Related projects ⓘ
Alternatives and complementary repositories for pyslingshot
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆60Updated 6 months ago
- ☆36Updated this week
- Python implementation of Milo for differential abundance testing on KNN graph☆60Updated last year
- Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.☆44Updated 4 months ago
- ☆44Updated last year
- Predict RNA velocity through deep learning☆64Updated 11 months ago
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆40Updated last year
- Multi-omic velocity inference☆107Updated last month
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- Single cell omics biology annotations☆48Updated 2 months ago
- Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.☆47Updated 4 months ago
- Non-parametric density inference for single-cell analysis.☆63Updated last week
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆57Updated 5 months ago
- ☆32Updated 2 months ago
- ☆32Updated 2 months ago
- R implementation of GeneTrajectory☆50Updated 7 months ago
- spatial transcriptome, single cell☆65Updated last year
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆105Updated 10 months ago
- ☆40Updated 6 months ago
- Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics☆28Updated 2 weeks ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆49Updated this week
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆58Updated last week
- Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).☆18Updated this week
- PhyloVelo, Phylogeny-based transcriptomic velocity of single cells☆40Updated last year
- Metacells - Single-cell RNA Sequencing Analysis☆96Updated last month
- Methods to compute Local Inverse Simpson's Index (LISI)☆58Updated 3 years ago
- Molecular interactions inference from single-cell multi-omics data☆22Updated 2 weeks ago
- Single-Cell Clustering Assessment Framework☆93Updated last year
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆38Updated 3 years ago
- Cell cycle inference in single-cell RNA-seq☆38Updated last year