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definition.yml
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definition.yml
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method:
id: celltrails
name: CellTrails
source: tool
platform: R
url: https://github.com/dcellwanger/CellTrails
authors:
- given: Daniel
family: Ellwanger
email: [email protected]
github: dcellwanger
manuscript:
doi: 10.1016/j.celrep.2018.05.002
google_scholar_cluster_id: '8451775467554180378'
publication_date: '2018-06-05'
container:
url: https://github.com/dynverse/ti_celltrails
docker: dynverse/ti_celltrails
wrapper:
type: cell_graph
topology_inference: free
trajectory_types:
- linear
- bifurcation
- convergence
- multifurcation
- tree
input_required: expression
parameters:
- id: filter_features
type: logical
default: false
description: Whether to include celltrails feature filtering
- id: threshold_dl
description: Minimum number of samples; if value < 1 it is interpreted as fraction,
otherwise as absolute sample count
type: integer
default: 2
distribution:
type: uniform
lower: 0
upper: 100
- id: threshold_cov
description: Minimum coefficient of variation; numeric value between 0 and 1
type: numeric
default: 0.05
distribution:
type: uniform
lower: 0
upper: 1
- id: threshold_ff
description: A Z-score cutoff
type: numeric
default: 1.7
distribution:
type: uniform
lower: 0
upper: 5
- id: min_expr
description: Minimum average feature expression
type: numeric
default: 0
distribution:
type: uniform
lower: 0
upper: 2
- id: frac
description: Fraction or number (if frac > 1) of eigengaps used to perform linear
fit.
type: numeric
default: 100
distribution:
type: expuniform
lower: 1
upper: 1000
- id: min_size
description: The initial cluster dedrogram is cut at an height such that the minimum
cluster size is at least min_size; if min_size < 1 than the fraction of total
samples is used, otherwise it is used as absoulte count
type: numeric
default: 0.01
distribution:
type: expuniform
lower: 0.001
upper: 1
- id: min_feat
description: Minimum number of differentially expressed features between siblings.
If this number is not reached, two neighboring clusters (siblings) in the pruned
dendrogram get joined.
type: integer
default: 5
distribution:
type: uniform
lower: 1
upper: 100
- id: max_pval
description: Maximum P-value for differential expression computation.
type: numeric
default: 0.0001
distribution:
type: expuniform
lower: 1.0e-07
upper: 1
- id: min_fc
description: Mimimum fold-change for differential expression computation
type: numeric
default: 2
distribution:
type: uniform
lower: 0
upper: 5
- id: l
description: Neighborhood size
type: integer
default: 10
distribution:
type: uniform
lower: 1
upper: 50