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How to cite QIAGEN Digital Insights products

Are you ready to publish your research using QIAGEN Digital Insights software? Here you can find guidelines and best practices for properly citing our tools.

In general, you are required to cite any images or results generated with QIAGEN Digital Insights products that are to be published in any form (e.g., print, electronic) as described below. If you have any questions, contact our Customer Support team at ts-bioinformatics@qiagen.com.

Citing QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA)

When citing QIAGEN IPA in your publication, choose the most appropriate option from the
sample text below.

Data were analyzed with the use of QIAGEN IPA (QIAGEN Inc., https://digitalinsights.qiagen.com/IPA).

The [networks, functional analyses, etc.] were generated through the use of QIAGEN IPA (QIAGEN Inc., https://digitalinsights.qiagen.com/IPA).

In addition, cite this paper describing the algorithms developed for use in QIAGEN IPA: 

Krämer, A., Green, J., Pollard, Jr., J., and Tugendreich, S. (2014) Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics. 30(4):523–30 

Citing QIAGEN Ingenuity Target Explorer

When citing QIAGEN Ingenuity Target Explorer in your publication, use the sample text below: 

The [pathways, targets, etc.] were generated through the use of QIAGEN Ingenuity Target Explorer (QIAGEN, Inc., https://targetexplorer.ingenuity.com/). 

Citing QIAGEN CLC Workbenches and QIAGEN CLC Server products

To cite a QIAGEN CLC Workbench or QIAGEN CLC Server product in general, cite our website. For example:

QIAGEN CLC Genomics Workbench (https://digitalinsights.qiagen.com)

For example, for QIAGEN CLC Genomics Workbench, version 9.5.3, can be cited as 

QIAGEN CLC Genomics Workbench, version 9.5.3 (https://digitalinsights.qiagen.com). 

Be sure to check the instructions for authors of the journal in which you intend to publish for their specific guidelines about citing websites. 

Additional information for citing QIAGEN CLC Genomics

Repeating your analysis

Reviewers who want to repeat your analysis can use versions of QIAGEN CLC Workbenches that are available for evaluation. These evaluation versions have a time-limited license and are fully functional. For more information, see the “Evaluation of CLC software” frequently asked questions at https://secure.clcbio.com/helpspot/index.php?pg=kb.chapter&id=72.

Information related to specific QIAGEN CLC Workbench or QIAGEN CLC Genomics Server analyses 

Background information relating to particular analyses can be found in our white papers and manuals. 

White papers 

Our white papers and application notes can be found at  https://digitalinsights.qiagen.com/science/technical-information/

For any analysis not covered by a white paper, refer to the manual of the product you used. 

Manuals 

The manuals are available in both *.html (online manual) and *.pdf format at https://digitalinsights.qiagen.com/technical-support/manuals/.

Referencing a particular QIAGEN CLC Genomics Workbench manual section is probably easiest using direct links to the online manual. To provide direct links to a particular section of a manual, open the “Online manual” version, navigate to the relevant section, and copy the link from your browser. 

Here is an example: Let’s say you need to refer to the QC for Sequencing Reads tool of QIAGEN CLC Genomics Workbench, version 21. Navigating to the section in the current version, copy the link. For example:

https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/curr ent/index.php?manual=QC_Sequencing_Reads.html

Citing QIAGEN OmicSoft software and Land database products

To cite QIAGEN OmicSoft products (software and Lands), the citation should contain the name of the QIAGEN OmicSoft product (QIAGEN OmicSoft Studio, QIAGEN OmicSoft Suite, QIAGEN OncoLand, etc.) used, the version number of software and/or the release date or version for Land data.

The following describes how to find version information.

  • For QIAGEN OmicSoft Studio: Analysis tab | Help | About OmicSoft Studio.
  • For QIAGEN OmicSoft Server: Server tab | Help | Check server version.
  • For a Land: Land tab | Select Land, and then hover the mouse over the Land used.

Examples:

Data from the cell lines were analyzed using QIAGEN OmicSoft Suite software, version 10.0.1.81.

Data analysis was performed on QIAGEN OmicSoft Studio software (QIAGEN, Redwood City, CA).

Expression data were extracted from QIAGEN OmicSoft DiseaseLand release HumanDisease_B37 20171220_v7.

Citing QIAGEN OmicSoft algorithms

OSA Aligner

For publications using our OSA (QIAGEN Omicsoft Aligner), cite the following paper:

Hu, J., Ge, H., Newman, M., and Liu, K. (2012) OSA: a fast and accurate alignment tool for RNA-Seq. Bioinformatics 28(14):1933–1934

FusionMap fusion detection

For publications using our fusion detection method, also cite our FusionMap paper:

Ge, H., Liu, K., Juan, T., Fang, F., Newman, M., and Hoeck, W. (2011) FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics 27(14):1922–1928

Oshell

For publications using our Oshell command, also cite the following paper:

Li, J., Hu, J., Newman, M., Liu. K., and Ge, H. (2014) RNA-Seq Analysis Pipeline Based on Oshell Environment. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): 973–978

Citing COSMIC and HGMD

If you refer to HGMD in any publication, cite with the following: 

Stenson, P.D., Mort, M., Ball, E.V., Shaw, K., Philips, A., and Cooper, D.N. (2014), The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics 133:1–9 (https://doi.org/10.1007/s00439-0131358-4)

If you refer to COSMIC in any publication, cite the website and the following paper:

Catalogue of Somatic Mutations in Cancer (COSMIC, cancer.sanger.ac.uk)

Tate, J.G, et al. (2019) COSMIC: the catalogue of somatic mutations in cancer.

Nucleic Acids Research 47(D1):D941–D947

(https://doi.org/10.1093/nar/gky1015)