phenopath
Genomic trajectory inference
A tool for inferring genomic trajectories from expression data with environmental and genetic covariates
Genomic trajectories (pseudotimes) in the presence of heterogenous environmental and genetic backgrounds
10 stars
3 watching
0 forks
Language: C++
last commit: over 5 years ago
Linked from 1 awesome list
seandavi/awesome-single-cellRelated projects:
| Repository | Description | Stars |
|---|---|---|
 jw156605/slicer | An R package implementing an algorithm for inferring cell trajectories based on gene expression data | 12 |
| kieranrcampbell/ouija | A probabilistic framework for inferring pseudotimes from single-cell gene expression data and understanding the underlying regulatory mechanisms. | 28 |
 kchen-lab/cyclum | A tool to identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations | 20 |
| kieranrcampbell/clonealign | A software package that uses Bayesian inference to assign gene expression estimates from single-cell RNA-seq and DNA-seq data to specific cancer clones. | 32 |
 dynverse/dynverse | Supports the development and benchmarking of trajectory inference methods in single-cell biology | 72 |
| kchen-lab/medalt | Software for inferring evolutionary lineage of tumor cells from single cell copy number profiles | 17 |
 ggiecold/eclair | An algorithmic framework for inferring cell lineages from gene expression data through multiple rounds of downsampling and clustering, followed by consensus clustering and graph construction. | 1 |
 phoenixding/scdiff | Analyzes single-cell RNA-seq data to predict cell differentiation trajectories and associated transcription factors and genes. | 28 |
 theislab/kbranches | A software package to identify regions of interest in single-cell differentiation trajectories | 5 |
 kstreet13/slingshot | An R package and Python implementation for analyzing developmental trajectories in single-cell RNA sequencing data | 270 |
 agrimgupta92/sgan | An implementation of a Generative Adversarial Network for predicting human trajectories in social scenarios. | 826 |
| kieranrcampbell/mfa | Infer bifurcations in single-cell data using Bayesian methods and hierarchical mixture modelling | 5 |
 umich-biostatistics/ibag | An R application for conducting Bayesian analyses of genomic models using a user-friendly interface. | 5 |
 amber-md/cpptraj | Tools for analyzing and processing molecular dynamics trajectory data | 137 |
 zjufanlab/spatalk | An R package that infers cell-cell communication and ligand-receptor-target networks from spatially resolved transcriptomic data | 62 |