Tools: TL#
Embeddings#
|
PHATE [Moon17]. |
|
Run Diffusion maps using the adaptive anisotropic kernel [Setty18]. |
|
TriMap: Large-scale Dimensionality Reduction Using Triplets [Amid19]. |
|
Self-Assembling Manifolds single-cell RNA sequencing analysis tool [Tarashansky19]. |
Clustering and trajectory inference#
|
PhenoGraph clustering [Levine15]. |
|
Harmony time series for data visualization with augmented affinity matrix at discrete time points [Nowotschin18i]. |
|
Wishbone identifies bifurcating developmental trajectories from single-cell data [Setty16]. |
|
Run Diffusion maps using the adaptive anisotropic kernel [Setty18]. |
|
Running Palantir |
Gene scores, Cell cycle#
|
Calculate marker pairs of genes. |
|
Assigns scores and predicted class to observations [Scialdone15] [Fechtner18]. |