This node is currently not available in KNIME v5.1 — instead we’re showing this page for KNIME v4.7. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.

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.

Popular Predecessors

Popular Successors

Views

This node has no views

Workflows

GASiCSeqAn

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

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: 2023-12-02

KNIME versions: From v3.6 to v4.7

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!