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Jump to:     qPCR     Mass spectrometry     Next-generation sequencing     Sanger sequencing     Fragment analysis     Synthetic biology     Utilities

qPCR   Learn more ›

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Design and Analysis

The Design and Analysis app offers the ability to create, edit, and analyze qPCR instrument files.


The Genotyping app includes improved visuals and integrated traces of allelic discrimination plots to allow thorough QC of SNP assays to accurately reflect the true signals versus background noise. 

High Resolution Melt (HRM) Analysis

The HRM app offers the ability to identify variation in nucleic acid sequences post-PCR using a high resolution melt curve. It features interlocking views for the melt curves and amplification plots, and the ability to analyze multiple runs at the same time.

Presence/Absence Analysis

The Presence/Absence app enables presence/absence testing in multiplex using a new Ct-based calling method and simple visualization tool. It supports 96- and 384-well plates- as well as the OpenArray™ format. 

Relative Quantification

The Relative Quantification app allows fast and powerful gene expression analysis with enhanced visual capabilities for relative quantification including: integrated correlation, volcano, and cluster analysis with the ability to drill down to amplification plots.

Standard Curve

The Standard Curve app offers reliable quantification of unknown quantities of genes and enables importing of standard curves from other experiments, providing analysis flexibility.

Instrument Connect App

Instrument Connect allows you to run your QuantStudio 3 and QuantStudio 5 Real-Time PCR Systems remotely. Use the mobile app to monitor your run progress or view amplification plots in real time. Plots can be filtered by sample or target.

The application connects to your instruments via Thermo Fisher Cloud.

Download from the Apple Store ›

Mass spectrometry

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Pathway Over-Representation Analysis

The Pathway Over-Representation Analysis app uses statistical analysis to detect biological pathways that are either over- or under-represented in a list of input proteins. The software accepts a list of protein identifiers as input and reports significant WikiPathways and optionally KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways associated with the list.

Sample Profiler

Sample Profiler identifies unknown compounds in high resolution accurate mass spectrometry sample data derived from defined populations. Once identified, these unknown compounds are compared against a database of representative compound profiles, complete with their chromatographic peak ranges. Data differences are analyzed via integrated hypothesis testing tools. Using this process, Sample Profiler elucidates how a new “challenge” sample differs from an existing representative profile; the app also measures how a sample population profile changes with time, location, production method, and more.

MS Instrument Connect

MS Instrument Connect provides the ability to monitor your LC-MS and GC-MS analyses remotely from any web-enabled device. Use this application to monitor real-time mass spectrometer status, track system utilization and historical events, and create email notifications to keep you informed when analytical runs are complete or when system errors occur. MS Instrument Connect is integrated with the Instrument Connect App, allowing you to track your systems from any iOS or Android device.

Next-generation sequencing

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Ion Reporter Software

Ion Reporter Software provides a suite of data analysis tools for variant detection, annotation, and reporting for the Ion PGM, Ion Proton, and Ion S5, and Ion S5 XL systems. The software identifies variants such as SNPs, indels, CNVs, and gene fusions, using preconfigured and customizable workflows optimized for Ion AmpliSeq panels. Using annotations from more than 20 public databases, including COSMIC, dbSNP, and OMIM, Ion Reporter Software has advanced filtering capabilities to focus on relevant variants. Visualization and reporting capabilities allow for sample comparison and creation of interpretive research reports for selected variants, and also identify complementary CE and TaqMan Assays for variants of interest.

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Sanger sequencing   Learn more ›

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Quality Check

The Quality Check app automatically checks CE sequence trace quality. It provides a results summary based on quality parameter settings and auto-flags lower quality traces for further inspection. Users can quickly and easily navigate to questionable or borderline data, and analyze, make adjustments, or exclude traces from the study.

Variant Analysis

The Variant Analysis app finds variants in samples sequenced on Applied Biosystems genetic analyzers. It reports variants at genomic coordinates and allows users to export variant calls in standard vcf format. It reports genomic annotations for SNPs and provides links to external databases.

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Next-Generation Confirmation

The Next-Generation Confirmation app confirms NGS variants using CE technology. It allows users to easily visualize the variants detected by both NGS and CE platforms and to export confirmed variants in standard vcf format.

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Fragment analysis

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Applied Biosystems Sizing Analysis Module, Peak Scanner Software

The Peak Scanner app is a DNA fragment sizing software that performs DNA fragment analysis, separates a mixture of DNA fragments according to their sizes, provides a profile of the separation, and precisely calculates the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using Applied Biosystems genetic analyzers.

Synthetic biology

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CRISPR Search and Design Tool

Use the CRISPR app to search our database of >600,000 predesigned CRISPR gRNAs or to analyze your sequence of interest for de novo gRNA designs for use in genome editing with CRISPR-Cas9 technology. The CRISPR module enables easy purchase of CRISPR-Cas9 and associated Thermo Fisher Scientific products.


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Cloud Connect Utility

The Cloud Connect Utility allows you to automatically upload files to Thermo Fisher Cloud by placing them in a folder on your  computer that is synced with the Cloud. Currently for Windows™ users only.

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More about the utility ›
 Instructions for installation and use ›