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Expand Barcode

HCS-Tools for KNIME version 4.0.0.v202007151505 by Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

This nodes takes a string column and appends the information content of the barcode string into several new columns (e.g. library code, library plate number, project code, assay, date, replicate).

The node uses a regular expression that tries to match the barcode column. Possible barcode patterns can be set at:
KNIME->Preferences->KNIME->HCS-Tools->Barcode patterns

This is an example:

Selected Barcode Pattern:(line breaks only for better visualization)
(?<libplatenumber>[0-9]{3})
(?<projectcode>[A-z]{2})
(?<date>[0-9]{6})
(?<replicate>[A-z]{1})
-
(?<libcode>[_A-z\d]{3})
(?<assay>[-_+\s\w\d]*)
Extracted metadata columns
Barcodes from input column library plate number project code date replicate library code assay
001AL100914C-CPW1nMovn 1 AL 100914 C CPW 1nMovn
006AL100914A-CPW1nMovn 6 AL 100914 A CPW 1nMovn
001MB140502D-KBI_lowGlucose 1 MB 140502 D KBI _lowGlucose

Each wanted meta information is marked as a named group and results in a new column.

Definition pattern: (?<groupname>regular expression)

The group name will be the name of the new column, beside a few exceptions:
group namecolumn name
libplatenumberlibrary plate number
libcodelibrary code
projectcodeproject code
concunitunit of concentration

Options

Barcode Column
The string column containing barcodes
Guess pattern
If activated, the node tries to find the best matching pattern from all available barcode patterns. (default)
If deactivated, the user need to select one of the listed barcode patterns.
Insert meta information behind
Select the column behind which the new meta information columns should appear.
Select <RowID> to put them first. Default values will be 'plateColumn' (if available) or the autoguessed barcode column.

Input Ports

Icon
Table with barcode column

Output Ports

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Input table with additional columns containing the extracted barcode metadata.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install KNIME HCS Tools from the following update site:

KNIME 4.3

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

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

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Developers

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