kstreet13 / slingshotView external linksLinks
Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
☆324Apr 23, 2024Updated last year
Alternatives and similar repositories for slingshot
Users that are interested in slingshot are comparing it to the libraries listed below
Sorting:
- TRAjectory-based Differential Expression analysis for SEQuencing data☆289Jun 17, 2025Updated 7 months ago
- AUCell: score single cells with gene regulatory networks☆183Mar 9, 2024Updated last year
- R package for detecting doublets in single-cell RNA sequencing data☆523Mar 21, 2025Updated 10 months ago
- Methods for detecting doublets in single-cell sequencing data☆230Updated this week
- R package for integrating and analyzing multiple single-cell datasets☆425Feb 4, 2026Updated last week
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆760Jan 6, 2024Updated 2 years ago
- Tools and methods for analysis of single cell assay data in R☆260Oct 17, 2025Updated 3 months ago
- ☆438Jan 8, 2026Updated last month
- R package implementation of Milo for testing for differential abundance in KNN graphs☆414Sep 4, 2025Updated 5 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆478Apr 5, 2024Updated last year
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆312Nov 1, 2022Updated 3 years ago
- NicheNet: predict active ligand-target links between interacting cells☆615Nov 12, 2025Updated 3 months ago
- Clone of the Bioconductor repository for the SingleR package.☆199Jan 5, 2026Updated last month
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆250Jan 10, 2026Updated last month
- Community-provided extensions to Seurat☆356Updated this week
- Python implementation of the Slingshot pseudotime algorithm☆69Oct 28, 2025Updated 3 months ago
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆234May 23, 2020Updated 5 years ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆620Oct 10, 2025Updated 4 months ago
- Interpretation of cell states using reference single-cell maps☆310Dec 19, 2025Updated last month
- RNA Velocity generalized through dynamical modeling☆487Dec 23, 2025Updated last month
- Multiome GRN inference.☆135Apr 19, 2024Updated last year
- Multi-sample multi-group scRNA-seq analysis tools☆218Dec 18, 2025Updated last month
- RNA velocity estimation in R☆194Sep 14, 2023Updated 2 years ago
- R package to infer biological activities from omics data using a collection of methods.☆285Dec 16, 2025Updated last month
- Interactively analyze single cell genomic data☆184Jan 14, 2026Updated last month
- Inferring CNV from Single-Cell RNA-Seq☆650Nov 14, 2025Updated 3 months ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆218Feb 26, 2024Updated last year
- ☆359Dec 9, 2021Updated 4 years ago
- R toolkit for the analysis of single-cell chromatin data☆406Jan 20, 2026Updated 3 weeks ago
- ☆270Oct 13, 2025Updated 4 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆231Aug 7, 2024Updated last year
- Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data☆152Feb 13, 2025Updated last year
- CellRank: dynamics from multi-view single-cell data☆427Updated this week
- R package for single cell and other data analysis using diffusion maps☆95Nov 9, 2025Updated 3 months ago
- Spatial omics analysis toolbox☆360Updated this week
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- Scissor package☆250May 10, 2024Updated last year
- Simple simulation of single-cell RNA sequencing data☆234Jan 12, 2026Updated last month
- Some tools for plotting single-cell data☆177May 17, 2025Updated 8 months ago