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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

CLC Genomics Workbench Biomedical Genomics Workbench

Advanced RNA-Seq

Advanced analysis of RNA-Seq experiments

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 Main Workbench CLC Genomics Workbench

Batch Rename

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

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

BioSignature Discoverer (Free Version)

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

CLC Main Workbench CLC Genomics Workbench Biomedical Genomics Workbench

BioSignature Discoverer (Full Version)

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

CLC Main Workbench CLC Genomics Workbench Biomedical Genomics Workbench

Bisulfite Sequencing

Tools to analyse bisulfite-converted reads.

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 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 CLC Genomics Workbench Biomedical Genomics Workbench

Bootstrapped ROC Viewer

Viewer for bROC (statistical analysis of differential expression)

CLC Main Workbench CLC Genomics Workbench Biomedical Genomics Workbench

CLC Genome Finishing Module

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

CLC Genomics Workbench Biomedical 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

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

GATK Integration

Access GATK best practice seamlessly from the Biomedical Genomics Workbench.

Biomedical Genomics Workbench

Histone ChIP-Seq

Tools for Histone ChIP-Sequencing

CLC Genomics Workbench Biomedical Genomics Workbench

Ingenuity Pathway Analysis

Upload statistical comparisons of expression data to Ingenuity Pathway Analysis

CLC Genomics Workbench Biomedical Genomics Workbench

Ingenuity Variant Analysis

Run workflows of analyses that include accessing Ingenuity Variant Analysis and the Allele Frequency Community

Biomedical Genomics Workbench

MetaGeneMark

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

CLC Genomics Workbench Biomedical Genomics Workbench

Mix-Square Transcript Quantification (Beta)

Mix-Square plug-in yields transcript concentration estimates from RNA-Seq data. In addition, the model can be used as an exploratory tool to investigate the positional (fragment) bias.

CLC Genomics Workbench Biomedical Genomics Workbench

PPfold

Parallel pfold implementation

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

QIAGEN GeneRead Panel Analysis Plugin

Identify and annotate variants in data generated with GeneRead DNAseq Gene Panels

Biomedical 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

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.

CLC Main Workbench CLC Genomics Workbench Biomedical 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

CLC Genomics Server Biomedical Genomics Server Solution

Advanced Peak Shape Tools Server Plugin (Beta)

Peak finding using shape information

CLC Genomics Server Biomedical Genomics Server Solution

Advanced RNA-Seq Server Plugin

Advanced analysis of RNA-Seq experiments

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

CLC Genomics Server Biomedical Genomics Server Solution

BioSignature Discoverer (Full Version)

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

CLC Genomics Server 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

GATK Integration Server Plugin

Access GATK best practice seamlessly from the Biomedical Genomics Workbench.

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

Upload statistical comparisons of expression data to Ingenuity Pathway Analysis

CLC Genomics Server Biomedical Genomics Server Solution

Ingenuity Variant Analysis Server Plugin

Run workflows of analyses that include accessing Ingenuity Variant Analysis and the Allele Frequency Community

Biomedical Genomics Server Solution CLC Genomics Server

Mix-Square Transcript Quantification Server Plugin (Beta)

Mix-Square plug-in yields transcript concentration estimates from RNA-Seq data. In addition, the model can be used as an exploratory tool to investigate the positional (fragment) bias.

CLC Genomics Server Biomedical Genomics Server Solution

QIAGEN GeneRead Panel Analysis Server Plugin

The QIAGEN GeneRead panel analysis server plugin

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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