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definition.yml
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definition.yml
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method:
id: urd
name: URD
tool_id: urd
source: tool
platform: R
url: https://github.com/farrellja/URD
license: GPL-3
authors:
- given: Jeffrey A.
family: Farrell
email: [email protected]
github: farrellja
manuscript:
doi: 10.1126/science.aar3131
google_scholar_cluster_id: '1243230199939989249'
publication_date: '2018-04-26'
container:
url: https://github.com/dynverse/ti_urd
docker: dynverse/ti_urd
wrapper:
type: trajectory
topology_inference: free
trajectory_types:
- linear
- bifurcation
- convergence
- multifurcation
- binary_tree
- tree
input_required:
- counts
- start_id
parameters:
- id: knn
type: integer
default: 0
distribution:
type: uniform
lower: 0
upper: 50
description: Number of nearest neighbors to use. `0` takes a guess.
- id: sigma.use
type: numeric
default: 0.0
distribution:
type: uniform
lower: 0.0
upper: 1.0
description: Kernel width to use for the diffusion map. `0` uses destiny's global auto-detection procedure.
- id: distance
type: character
default: euclidean
values:
- euclidean
- cosine
- rankcor
description: Distance metric to use for determining transition probabilities.
- id: n_floods
type: integer
default: 20
distribution:
type: uniform
lower: 5
upper: 50
description: Number of simulations to perform and average.
- id: stability.div
type: numeric
default: 10
distribution:
type: uniform
lower: 2
upper: 50
description: Number of simulation subsamplings to calculate.
- id: mp.factor
type: numeric
default: 1
distribution:
type: uniform
lower: 0
upper: 10
description: Retain PCs than are this factor more than the estimated maximum singular value expected or random data. This is useful in cases when there are many PCs that have standard deviations just above that expected by random, which probably represent noise and should be excluded.
- id: perplexity
type: numeric
default: 30
distribution:
type: uniform
lower: 0
upper: 100
description: Perplexity parameter for the tSNE.
- id: theta
type: numeric
default: 0.5
distribution:
type: uniform
lower: 0
upper: 1
description: Speed/accuracy trade-off for Barnes-Hut approximation of tSNE. 0 is exact tSNE, higher is less accurate.
- id: max_iter
type: integer
default: 1000
distribution:
type: expuniform
lower: 100
upper: 10000
description: Number of nearest neighbors to use. `0` takes a guess.
- id: num.nn
type: integer
default: 30
distribution:
type: expuniform
lower: 10
upper: 100
description: How many nearest-neighbors to use in the k-nn graph.
- id: do.jaccard
type: logical
default: TRUE
description: Weight edges in the k-nn graph according to their Jaccard overlap?
- id: optimal.cells.forward
type: numeric
default: 20
distribution:
type: expuniform
lower: 5
upper: 100
description: The number of cells in the direction specified by pseudotime.direction at which the logistic should reach 1-asymptote.
- id: max.cells.back
type: numeric
default: 40
distribution:
type: expuniform
lower: 5
upper: 200
description: The number of cells in the direction opposite from that specified by pseudotime.direction at which the logistic should reach asymptote.
- id: n.per.tip
type: integer
default: 25000
distribution:
type: expuniform
lower: 100
upper: 1000000
description: Number of walks to do per tip.
- id: root.visits
type: integer
default: 1
distribution:
type: uniform
lower: 1
upper: 5
description: Number of steps to take that visit a root.cell before stopping.
- id: max.steps
type: integer
default: 25000
distribution:
type: expuniform
lower: 100
upper: 1000000
description: Number of walks to do per tip.
- id: n.subsample
type: integer
default: 10
distribution:
type: expuniform
lower: 2
upper: 100
description: Number of subsamplings to perform for calculating stability.
- id: divergence.method
type: character
default: ks
values:
- ks
- preference
description: Distance metric to use for determining transition probabilities.
- id: cells.per.pseudotime.bin
type: integer
default: 80
distribution:
type: expuniform
lower: 10
upper: 1000
description: Approximate number of cells to assign to each pseudotime bin for branchpoint finding.
- id: bins.per.pseudotime.window
type: integer
default: 5
distribution:
type: uniform
lower: 2
upper: 20
description: Width of moving window in pseudotime used for branchpoint finding, in terms of bins.
- id: p.thresh
type: numeric
default: 0.01
distribution:
type: expuniform
lower: 0.00001
upper: 1
description: p-value threshold to use in determining whether visitation is significantly different from pairs of tips