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Workbench plugins

PluginManualSupported onDownloadDeveloper

Additional Alignments

Perform alignments with ClustalO, ClustalW and MUSCLE

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

Advanced Peak Shape Tools Plugin (Beta)

Peak finding using shape information

Biomedical Genomics Workbench CLC 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 Main Workbench CLC Genomics Workbench

Batch Rename

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

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

BioSignature Discover (Basic Version)

BioSignature Discover is a complete statistical analysis pipeline for performing feature selection, identifying and interpreting predictive or diagnostic signatures in molecular data.

CLC Main Workbench Biomedical Genomics Workbench CLC Genomics Workbench

BioSignature Discover (Demo Version)

BioSignature Discover is a complete statistical analysis pipeline for performing feature selection, identifying and interpreting predictive or diagnostic signatures in molecular data.

CLC Main Workbench Biomedical Genomics Workbench CLC Genomics Workbench

BioSignature Discover (Full Version)

BioSignature Discover is a complete statistical analysis pipeline for performing feature selection, identifying and interpreting predictive or diagnostic signatures in molecular data.

CLC Main Workbench Biomedical Genomics Workbench CLC Genomics Workbench

BioSignature Discover (Professional Version)

BioSignature Discover is a complete statistical analysis pipeline for performing feature selection, identifying and interpreting predictive or diagnostic signatures in molecular data.

CLC Main Workbench Biomedical Genomics Workbench CLC Genomics Workbench

Bisulfite Sequencing

Tools to analyse bisulfite-converted reads.

Biomedical Genomics Workbench CLC 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 Main Workbench CLC Genomics Workbench

Blast2GO PRO Viewer

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

CLC Main Workbench CLC Genomics Workbench

Bookmark Navigator

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

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

Bootstrapped ROC

Statistical analysis of differential expression.

CLC Main Workbench Biomedical Genomics Workbench CLC Genomics Workbench

Bootstrapped ROC Viewer

Viewer for bROC (statistical analysis of differential expression)

CLC Main Workbench Biomedical Genomics Workbench CLC Genomics Workbench

CLC Genome Finishing Module

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

Biomedical Genomics Workbench CLC Genomics Workbench

CLC MLST Module

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

CLC Main Workbench CLC Genomics Workbench

CLC Microbial Genomics Module

CLC Microbial Genomics Module

Biomedical Genomics Workbench CLC Genomics Workbench

CLC Workbench Client Plugin

Client plugin for connecting to a CLC Server. Compatible with the CLC Genomics Server 8.x.x and CLC Bioinformatics Database 4.7.x.

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

Cytognomix Dependencies HG18

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

Biomedical Genomics Workbench CLC Genomics Workbench

Cytognomix Dependencies HG19

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

Biomedical Genomics Workbench CLC Genomics Workbench

Cytognomix Shannon Pipeline

Shannon human splicing pipeline for use in a CLC Genomics Workbench

Biomedical Genomics Workbench CLC Genomics Workbench

Cytognomix Shannon Pipeline Client

Shannon human splicing pipeline for use in a CLC Genomics Workbench

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

Histone ChIP-Seq

Tools for Histone ChIP-Sequencing

Biomedical Genomics Workbench CLC Genomics Workbench

Ingenuity Pathway Analysis

Ingenuity Pathway Analysis plug-in

Biomedical Genomics Workbench CLC Genomics Workbench

Ingenuity Variant Analysis

Access QIAGEN's Ingenuity Variant Analysis and the Allele Frequency Community seamlessly from the Biomedical Genomics Workbench.

Biomedical Genomics Workbench

MetaGeneMark

MetaGeneMark plugin is a fast implementation of a popular ab initio method for finding protein coding genes in metagenomes.

Biomedical Genomics Workbench CLC Genomics Workbench

OncoMD

OncoMD Additions

Biomedical Genomics Workbench CLC Genomics Workbench

PPfold

Parallel pfold implementation

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

Paracel BLAST Evaluation

Paracel BLAST Evaluation

CLC Main Workbench CLC Genomics Workbench CLC Drug Discovery 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. This plugin will not be available for the CLC Genomics Workbench 9.0 and higher. Please consider using the RNA-seq tools provided under the Toolbox | Transcriptomics Analysis area instead of using the tool provided by this plugin.

CLC Genomics Workbench

Rapid Neighbour-Joining

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

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

Sequence Reader

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

CLC Main Workbench CLC Genomics Workbench

SignalP

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

CLC Main Workbench CLC Genomics Workbench CLC Drug Discovery Workbench

TMHMM

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

CLC Main Workbench CLC Genomics Workbench CLC Drug Discovery Workbench

TRANSFAC TFBS

The TRANSFAC TFBS extension can be used to search for putative transcription factor binding sites in DNA sequences. This release bundles release 2015.2 of the Biobase TRANSFAC matrix profiles and reports.

CLC Main Workbench Biomedical Genomics Workbench CLC Genomics 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 Main Workbench CLC Genomics Workbench

Vector NTI import

Vector NTI data import functionality.

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

Server plugins

PluginManualSupported onDownloadDeveloper

Additional Alignments Server Plugin

Perform alignments with ClustalO, ClustalW and MUSCLE

Biomedical Genomics Server Solution

Advanced Peak Shape Tools Server Plugin (Beta)

Peak finding using shape information

CLC Genomics Server Biomedical Genomics 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

Biomedical Genomics Server Solution

BioSignature Discover (Full Version)

BioSignature Discover is a complete statistical analysis pipeline for performing feature selection, identifying and interpreting predictive or diagnostic signatures in molecular data.

Biomedical Genomics Server Solution

Bisulfite Sequencing Server Plugin

Tools to analyse bisulfite-converted reads.

CLC Genomics Server Biomedical Genomics Server Solution

CLC Genome Finishing Server Extension

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

CLC Genomics Server Biomedical Genomics Server Solution

CLC Microbial Genomics Server Extension

CLC Microbial Genomics Server Extension

CLC Genomics Server Biomedical Genomics Server Solution

Cytognomix Shannon Pipeline Server

Shannon human splicing pipeline for use on a CLC Genomics Server

CLC Genomics Server Biomedical Genomics Server Solution

Histone ChIP-Seq Server Plugin

Tools for Histone ChIP-Sequencing

CLC Genomics Server Biomedical Genomics Server Solution

Ingenuity Pathway Analysis Server Plugin

Ingenuity Pathway Analysis Server Plug-in

CLC Genomics Server Biomedical Genomics Server Solution

Ingenuity Variant Analysis Server Plugin

Access Ingenuity Variant Analysis and the Allele Frequency Community via a CLC Server

Biomedical Genomics Server Solution CLC Genomics Server

Paracel BLAST Server

Paracel BLAST Server

CLC Genomics Server Biomedical Genomics Server Solution

QIAGEN GeneRead Panel Analysis Server Plugin

The QIAGEN GeneRead panel analysis server plugin

Biomedical Genomics Server Solution

RNA-Seq Legacy Server Plugin

Legacy version of the RNA-seq algorithm. This plugin will not be available for the CLC Genomics Server 8.0 and higher. Please consider using the inbuilt RNA-seq tool instead of using the tool provided by this plugin.

CLC Genomics Server Biomedical Genomics Server Solution

Read Mapping Legacy Server Plugin

CLC Genomics Server Biomedical Genomics 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 Biomedical Genomics Server Solution

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