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GASiC

GASiC version 0.1.0.v202007161536 by Stephan Aiche

Read correction node for the GASiC approach. The node takes a normalized read count vector and a similarity matrix for the genomes and computes a corrected abundance vector for the given species.

Options

Cobyla Options

Rho Begin
Initial Variables Change.
Rho End
Convergence criteria.
Max. Iterations
Maximal number of iterations for the optimization.

Bootstrapping Options

Number of iterations
Number of bootstrap samples.

p-value computation

test level
Abundance from species are treated as not present. Needed for p-value computation.

Mutlithreading Options

Number of Threads
The number of threads that should be used to optimize the correction values.

Input Ports

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Table containing for each read the information to which genomes it maps.
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Table containing for simulated reads from which genome they were simulated and to which genomes they map.

Output Ports

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Corrected abundance values.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install GASiC Nodes for KNIME from the following update site:

KNIME 4.4

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Developers

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