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definition.yml
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definition.yml
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method:
id: cellrouter
name: CellRouter
source: tool
platform: R
url: https://github.com/edroaldo/cellrouter
authors:
- given: Edroaldo
family: Lummertz da Rocha
github: edroaldo
ORCID: 0000-0003-0537-4223
- given: James J.
family: Collins
email: [email protected]
ORCID: 0000-0003-0537-4223
- given: George Q.
family: Daley
manuscript:
doi: 10.1038/s41467-018-03214-y
google_scholar_cluster_id: '16330849752690040143'
publication_date: '2018-03-01'
container:
url: https://github.com/dynverse/ti_cellrouter
docker: dynverse/ti_cellrouter
wrapper:
type: cell_graph
topology_inference: free
trajectory_types:
- linear
- bifurcation
- convergence
- multifurcation
- binary_tree
- tree
input_required:
- expression
- start_id
parameters:
- id: ndim_pca
description: Number of principal components to compute
type: integer
default: 20
distribution:
type: uniform
lower: 2
upper: 100
- id: ndim_tsne
description: Number of tsne dimensions to compute
type: integer
default: 11
distribution:
type: uniform
lower: 2
upper: 100
- id: max_iter
description: Maximal number of tsne iterations
type: integer
default: 1000
distribution:
type: expuniform
lower: 100
upper: 100000
- id: cluster_method
description: Method to use for clustering
type: character
values:
- graph.clustering
- model.clustering
default: graph.clustering
- id: k_clustering
description: Number of nearest neighbors to build a k-nearest neighbors graph
for clustering
type: integer
default: 20
distribution:
type: uniform
lower: 2
upper: 1000
- id: ndim_pca_clustering
description: Number of PCA dimensions used for k-nearest neighbors graph for clustering
type: integer
default: 20
distribution:
type: uniform
lower: 2
upper: 100
- id: k_knn
description: Number of nearest neighbors to build a k-nearest neighbors graph
for knn
type: integer
default: 10
distribution:
type: expuniform
lower: 2
upper: 1000
- id: ndim_pca_knn
description: Number of PCA dimensions used for knn
type: integer
default: 20
distribution:
type: uniform
lower: 2
upper: 100
- id: sim_type
description: Similarity type for knn
type: character
default: jaccard
values: jaccard
- id: distance_method_paths
description: Distance method for paths
type: character
default: graph
values:
- euclidean
- maximum
- manhattan
- canberra
- binary
- graph
- id: ranks
description: How to rank the paths
type: character
default: rank
values:
- path_cost
- path_flow
- rank
- length
- id: num_cells
description: Trajectories should contain at least num.cells
type: integer
default: 3
distribution:
type: uniform
lower: 3
upper: 100
- id: neighs
description: The size of the neighborhood in kNN graph used to smoothen kinetic
profiles
type: integer
distribution:
type: uniform
lower: 2
upper: 100
default: 3
- id: perplexity
description: Perplexity parameter for tsne
type: numeric
default: 30
distribution:
type: uniform
lower: 5
upper: 100