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GASiC

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

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

Output Ports

: Corrected abundance values.

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Workflows

GASiCSeqAn

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Installation

To use this node in KNIME, install the extension GASiC Nodes for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Stephan Aiche

Plugin version: 0.1.0.v202007161536

On NodePit since: 2022-12-06

Last update: 2024-11-09

KNIME versions: From v3.6 to v4.7

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