scdiff
Trajectory analyzer
Analyzes single-cell RNA-seq data to predict cell differentiation trajectories and associated transcription factors and genes.
28 stars
3 watching
5 forks
Language: Python
last commit: over 4 years ago
Linked from 1 awesome list
seandavi/awesome-single-cellRelated projects:
| Repository | Description | Stars |
|---|---|---|
 kstreet13/slingshot | An R package and Python implementation for analyzing developmental trajectories in single-cell RNA sequencing data | 270 |
 dimenwarper/scimitar | Analyzes single-cell measurements to infer morphing trajectories and their associated regulation. | 7 |
 theislab/kbranches | A software package to identify regions of interest in single-cell differentiation trajectories | 5 |
 qifeidkn/stagate | A software framework for learning spatial embeddings from high-dimensional transcriptomics data using an adaptive graph attention auto-encoder | 37 |
 kchen-lab/cyclum | A tool to identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations | 20 |
| theislab/scvelo | Analyzes single-cell RNA velocity data to infer cellular dynamics and regulatory changes | 418 |
 dynverse/dynverse | Supports the development and benchmarking of trajectory inference methods in single-cell biology | 72 |
| theislab/pseudodynamics | A software framework for analyzing single-cell RNA-seq time series data to infer population dynamics. | 39 |
 d-seams/seams-core | Analyzes molecular dynamics trajectories to infer structural properties of molecules | 35 |
 rabadanlab/sctda | An object-oriented Python library for analyzing single-cell RNA-seq data using topological representations | 7 |
 jw156605/slicer | An R package implementing an algorithm for inferring cell trajectories based on gene expression data | 12 |
 lingfeiwang/normalisr | A software framework for analyzing single-cell RNA sequencing data | 18 |
 scverse/scanpy | A Python toolkit for analyzing large-scale single-cell gene expression data | 1,919 |
 peterzzq/scdart | A deep learning framework designed to integrate multi-modal single cell data from different modalities while preserving cell trajectory structures. | 10 |
| scverse/scvi-tools | Probabilistic analysis tools for single-cell omics data | 1,251 |