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Workbench plugins

PluginManualSupported onDownloadDeveloper

Additional Alignments

Perform alignments with ClustalO, ClustalW and MUSCLE

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Sequence Viewer CLC Main Workbench

Advanced Peak Shape Tools Plugin (Beta)

Peak finding using shape information

CLC Genomics Workbench Biomedical Genomics Workbench

Annotate with GFF file

Using this plug-in it is possible to annotate a sequence from list of annotations found in a GFF file
Located in the Toolbox.

CLC Genomics Workbench CLC Main Workbench

Batch Rename

Rename files in batch by adding a prefix or a number.

CLC Drug Discovery Workbench CLC Genomics Workbench Biomedical Genomics Workbench CLC Sequence Viewer CLC Main Workbench

Biobase Genome Trax Annotate

Create tracks with various data from Biobase Genome Trax

CLC Genomics Workbench Biomedical Genomics Workbench

Biobase Genome Trax Download

Create tracks with various data from Biobase Genome Trax

CLC Genomics Workbench Biomedical Genomics Workbench

Blast2GO PRO

Blast2GO PRO is an all-in-one tool for functional annotation of (novel) sequences and the analysis of annotation data.

CLC Genomics Workbench Biomedical Genomics Workbench CLC Main Workbench

Blast2GO Viewer

Blast2GO Viewer is a free plug-in to view Blast2GO project file generated with the commercial Blast2GO PRO plug-in.

CLC Genomics Workbench Biomedical Genomics Workbench CLC Main Workbench

Bookmark Navigator

With this extension you can bookmark elements in the Navigation Area.

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Sequence Viewer CLC Main Workbench

Bootstrapped ROC

Statistical analysis of differential expression.

CLC Genomics Workbench Biomedical Genomics Workbench CLC Main Workbench

Bootstrapped ROC Viewer

Viewer for bROC (statistical analysis of differential expression)

CLC Genomics Workbench Biomedical Genomics Workbench CLC Main Workbench

CLC MLST Module

MLST Module makes it easy and fast to do MultiLocus Sequence Typing.

CLC Genomics Workbench CLC Main Workbench

CLC Microbial Genome Finishing Module

Various tools for genome finishing aimed to close and produce high quality genomes in sequencing projects.

CLC Genomics Workbench

CLC Workbench Client Plugin

Client plugin for connecting to a CLC Genomics Server, CLC Drug Discovery Server or Bioinformatics Database. The plug-in also includes Grid Engine Integration.

CLC Drug Discovery Workbench CLC Genomics Workbench Biomedical Genomics Workbench CLC Main Workbench

Cytognomix Dependencies HG18

Dependencies required by the Shannon human splicing pipeline (NCBI36/hg18)

CLC Genomics Workbench Biomedical Genomics Workbench

Cytognomix Dependencies HG19

Dependencies required by the Shannon human splicing pipeline (GRCh37/hg19)

CLC Genomics Workbench Biomedical Genomics Workbench

Cytognomix Shannon Pipeline

Shannon human splicing pipeline for use in a CLC Genomics Workbench

CLC Genomics Workbench Biomedical Genomics Workbench

Cytognomix Shannon Pipeline Client

Shannon human splicing pipeline for use in a CLC Genomics Workbench

CLC Genomics Workbench Biomedical Genomics Workbench

Duplicate Reads Removal (Beta)

Detects and removes duplicate reads

CLC Genomics Workbench

External Applications Client Plugin

Run external applications on a CLC Server via the Workbench menu system. External applications are made available by a Server admin configuring them in the CLC Server web interface.

CLC Drug Discovery Workbench CLC Genomics Workbench Biomedical Genomics Workbench CLC Main Workbench

Ingenuity Pathway Analysis

Ingenuity Pathway Analysis plug-in

CLC Genomics Workbench Biomedical Genomics Workbench

Ingenuity Variant Analysis

Run Ingenuity Variant Analysis and look at the results in the Workbench and in Ingenuity Variant Analysis.

Biomedical Genomics Workbench

Metadata Import (Beta)

Import metadata from a tabular file, or associate data already imported with metadata from a tabular file.

CLC Genomics Workbench CLC Main Workbench

PPfold

Parallel pfold implementation

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Sequence Viewer CLC Main Workbench

Paracel BLAST Evaluation

Paracel BLAST Evaluation

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Main Workbench

QIAGEN GeneRead Panel Analysis Plugin

The QIAGEN GeneRead panel analysis plugin

Biomedical Genomics Workbench

RNA-Seq Legacy

Legacy version of the RNA-seq algorithm.

CLC Genomics Workbench

Rapid Neighbour-Joining

A fast and memory efficient implementation of the Neighbour-Joining method with fast distance estimation.

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Sequence Viewer CLC Main Workbench

Read Mapping Legacy

Legacy version of the QIAGEN Aarhus Read Mapper algorithm

CLC Genomics Workbench

Recent Items Navigator

With this extension you can keep track of recently used items in the Navigator Area.

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Sequence Viewer CLC Main Workbench

Sequence Reader

The sequence reader can be used to read aloud a part of a sequence.

CLC Genomics Workbench CLC Main Workbench

SignalP

Integrated signal peptide prediction using SignalP 4.1 at http://www.cbs.dtu.dk/services/SignalP.
(Requires an Internet connection).

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Main Workbench

TMHMM

Integrated transmembrane helix prediction using TMHMM at http://www.cbs.dtu.dk/services/TMHMM.
(Requires an Internet connection).

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Main Workbench

TRANSFAC TFBS

The TRANSFAC TFBS extension can be used to search for putative transcription factor binding sites in DNA sequences. This release is based on the 2014.4 release of the Biobase TRANSFAC matrix profiles.

CLC Genomics Workbench Biomedical Genomics Workbench CLC Main Workbench

Transcript Discovery (Beta)

The transcript discovery plug-in enables you to map RNA-Seq reads to a genomic reference and predicts transcripts and genes.

CLC Genomics Workbench

Transfac (Free)

The TRANSFAC extension can be used to search for putative transcription factor binding sites in DNA sequences.

CLC Genomics Workbench CLC Main Workbench

Vector NTI import

Vector NTI data import functionality.

CLC Drug Discovery Workbench CLC Genomics Workbench CLC Sequence Viewer CLC Main Workbench

Server plugins

PluginManualSupported onDownloadDeveloper

Additional Alignments Server Plugin

Perform alignments with ClustalO, ClustalW and MUSCLE

CLC Genomics Server CLC Cancer Research Server Solution

Advanced Peak Shape Tools Server Plugin (Beta)

Peak finding using shape information

CLC Genomics Server CLC Cancer Research Server Solution

Annotate with GFF file server plugin

Using this plug-in it is possible to annotate a sequence from list of annotations found in a GFF file

CLC Genomics Server CLC Cancer Research Server Solution

Biobase GenomeTrax Server Plugin

Biobase GenomeTrax Server Plugin

CLC Genomics Server CLC Cancer Research Server Solution

Convert Variant Tracks Server Plugin

This plugin lets you convert old variations tracks to new variant tracks.

CLC Genomics Server CLC Cancer Research Server Solution

Copy Number Variant Detection Server (Beta)

Detects copy number variations

CLC Cancer Research Server Solution

Cytognomix Shannon Pipeline Server

Shannon human splicing pipeline for use on a CLC Genomics Server

CLC Genomics Server CLC Cancer Research Server Solution

Duplicate Mapped Reads Removal Server Plugin (Beta)

Duplicate Mapped Reads Removal

CLC Cancer Research Server Solution CLC Genomics Server

Duplicate Reads Removal Server Plugin (Beta)

Detects and removes duplicate reads

CLC Genomics Server CLC Cancer Research Server Solution

Ingenuity Pathway Analysis Server Plugin

Ingenuity Pathway Analysis Server Plug-in

CLC Genomics Server CLC Cancer Research Server Solution

Ingenuity Variant Analysis Server Plugin

Ingenuity Variant Analysis Server plug-in

CLC Genomics Server CLC Cancer Research Server Solution

Map Reads to Reference Affine Server Plugin (Beta)

A fast and memory efficient read mapper with affine gap cost

CLC Genomics Server CLC Cancer Research Server Solution

Paracel BLAST Server

Paracel BLAST Server

CLC Genomics Server CLC Cancer Research Server Solution

QIAGEN GeneRead Panel Analysis Server Plugin

The QIAGEN GeneRead panel analysis server plugin

CLC Cancer Research Server Solution

RNA-Seq Legacy Server Plugin

Legacy version of the RNA-seq algorithm.

CLC Genomics Server CLC Cancer Research Server Solution

Read Mapping Legacy Server Plugin

CLC Genomics Server CLC Cancer Research Server Solution

Transcript Discovery Server Plugin (Beta)

The transcript discovery plug-in enables you to map RNA-Seq reads to a genomic reference and predicts transcripts and genes.

CLC Genomics Server CLC Cancer Research Server Solution

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