Connect Data Analysis Apps

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Animal Health VeriVet Software qPCR

The VeriVet app allows the user to create a plate layout, generate a template file for import to the real-time PCR instrument, and remotely monitor the instrument run (Quantstudio™ 5 Real-Time PCR System). The software can be used to automatically analyze results to generate an easy read out of positive, negative, suspect and inconclusive PCR calls (Quantstudio 5 Real-Time PCR System and Applied Biosystems™ 7500 / 7500 Fast).

The VeriVet Software is compatible with all VetMAX™ kits and with Applied Biosystems 7500 / 7500 Fast and Quantstudio 5 Real-Time PCR Systems.

Design and Analysis

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

Genotyping

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

This High Resolution Melt Analysis (HRM) app is designed for post-PCR analysis to identify variation in nucleic acid sequences. The method is based on detecting small differences in PCR melting (dissociation) curves. It is enabled by high-brightness, dsDNA-binding dyes used in conjunction with real-time PCR instrumentation that has precise temperature ramp control, advanced data capture capabilities, and access to software designed specifically for HRM analysis.

hPSC Scorecard Analysis

The hPSC Scorecard Analysis app scores gene expression profiles generated using the TaqMan hPSC Scorecard Panel compared to a reference set of well-characterized pluripotent stem cell lines. It provides raw data as well as box plots, heat maps, and correlation plots for export.

Presence/Absence Analysis

The Presence Absence Analysis app analyzes and interprets real-time PCR data or post-read data to determine if a specific target sequence is present (presence) or not present (absence) in a sample. It provides an easy-to-view presence/absence result in a plate grid view.

Relative Quantification

The Relative Quantification app allows fast and powerful gene expression analysis with enhanced visual capabilities for relative quantification including integrated correlation and 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.

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 also reports genomic annotations for SNPs and provides links to external databases.

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.

SeqStudio Plate Manager 

The SeqStudio Plate Manager app enables the user to set up plates and configure different application-type runs for the Applied Biosystems SeqStudio Genetic Analyzer. It also supports remote monitoring and remote control of runs.

Peak Scanner

The Peak Scanner app offers peak identification and fragment sizing for application-specific capillary electrophoresis assays.

New Microsatellite Analysis

The Microsatellite Analysis app is microsatellite genotyping software that allows you to analyze a mixture of DNA fragments, separated by size. This analysis provides a profile of the separation, precisely calculates the sizes of the fragments, and determines the microsatellite alleles present in the sample. Microsatellite analysis is commonly used to study Microsatellite Instability in cancer and Triplet Repeat Expansion in neurodegenerative diseases, and for Species Identification & Characterization and Human Sample Authentication.

Ion Reporter

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 pre-configured and customizable workflows optimized for Ion AmpliSeq panels. Using annotations from >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. Also, identify complementary CE and TaqMan Assays for variants of interest.

PCR Designer

The PCR Designer module offers the ability to create and edit thermal protocols for SimpliAmp & ProFlex endpoint PCR instruments.

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.

GeneArt QA

Use this module to browse, download and share Quality Assurance Documentation (QAD) for all your orders from GeneArt. Note that only QAD for orders shipped after you confirmed the Terms Of Use for the service will be uploaded and made available for review.

GeneArt™ Strings™ Assistant

The GeneArt™ Strings™ Assistant makes it easy to order your DNA sequences as GeneArt Strings DNA fragments.

Invitrogen™ CRISPR Array Designer 

Use The Invitrogen™ CRISPR Array Designer Tool to design large number of CRISPRs for cell engineering experiment(s). The software will also assist customers in arranging oligonucleotides (containing CRISPR guide-RNAs) on 96-well plates. This is not associated with any instrument but has the underlying algorithm used by the GeneArt CRISPR Search and Design Tool. All of these products can be ordered by customers from Thermo Fisher Scientific.

Oligo Perfect 

Use the OligoPerfect™ designer to design oligonucleotide primers for your PCR-dependent experiments. In addition to designing primers, the OligoPerfect™ designer enables easy purchase of oligonucleotides by Thermo Fisher Scientific.

Sequence Viewer 

The Sequence Viewer module will allow users to load DNA sequence files and view relevant molecule information visually. Molecule features can be viewed as annotated sequences in intuitive graphical and sequence maps.

TAL

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

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.

Almanac App

Almanac enables remote monitoring of your LC-MS and GC-MS systems to increase your productivity and let you focus on other activities. See what is happening in real time or receive e-mail notifications of analysis progress. Document system maintenance and or schedule instrument access time. The application also allows you to send device-specific information to support teams for troubleshooting, without sending any raw data, sample, or personal information, increasing instrument uptime.

Omics Comparator

The Omics Comparator analysis software generates Venn diagrams to compare up to 5 lists of input proteins. The analysis can also work on lists of genes. The software displays set membership together with molecular annotations including color coded Gene Ontology terms.

My Pipette™ Connect Utility

The My Pipette Connect Utility for Windows enables E1-ClipTip electronic pipettes to link with the My Pipette Creator app. Please download and install to get started. The My Pipette Creator app helps to increase productivity by leveraging the power of the Connect platform and the connectivity feature of the E1-ClipTip electronic pipette. This app allows users to efficiently create pipetting programs, collaborate by sharing programs with colleagues, and update pipette firmware. Programs can be easily transferred to and from the E1-ClipTip wirelessly or via a USB connection. Additionally, pre-written and validated protocols designed specifically for Thermo Fisher assays and kits are available which can dramatically reduce experiment setup time and minimize potential errors. For more information, please visit thermofisher.com/mypipette

My Pipette™ Creator 

The My Pipette Creator app helps to increase productivity by leveraging the power of the Connect platform and the connectivity feature of the E1-ClipTip electronic pipette. This app allows users to efficiently create pipetting programs, collaborate by sharing programs with colleagues, and update pipette firmware. Programs can be easily transferred to and from the E1-ClipTip wirelessly or via a USB connection. Additionally, pre-written and validated protocols designed specifically for Thermo Fisher assays and kits are available which can dramatically reduce experiment setup time and minimize potential errors. For more information, please visit thermofisher.com/mypipette

ViroScore®-HIV

The HIV Sanger software & database solution to perform genotyping and subtyping analyses, and measure potential impact on disease probability through more than 7 regularly updated algorithms, organized into easy-to-use reports.

CosmosID

CosmosID's platform identifies bacteria and viruses in a whole genome shotgun metagenomic sample and is able to discriminate pathogens from their ‘near neighbors’ using statistical and computational methods, with no prior assumptions as to what is present in the sample.

NanoDrop 

The NanoDrop app gives you the flexibility to view and work with dsDNA, ssDNA and RNA data acquired with the NanoDrop One and the NanoDrop 2000 instruments on any device. You can access all of the Acclaro Sample Intelligence Technology information associated with your NanoDrop One data. Contaminant information can be displayed and reviewed with an interactive spectral display.

OMNIC™ Anywhere

The OMNIC™ Anywhere app allows you to extract the content of an SPA file and visualize its data within an interactive spectral display. You can perform basic operations on it, such as find the peaks of the spectrum trace and download its graph view as an image ready to be included in your reports.

Virtual TruScan RM (VTR) App

The Virtual TruScan RM (VTR) App allows you to use the TruScan RM algorithm in the cloud to validate methods testing method selectivity and robustness using uploaded Run files as virtual samples without the need for a physical sample.

iBright Image Analysis Software

iBright Image Analysis (iBA) software is an easy to use application for automated data analysis and management of digital images depicting electrophoresis gels and blots. The software can be used for editing images (e.g., to adjust brightness/contrast, rotation, crop, false coloring, etc) as well as identification and quantitation of bands, background subtraction, relative and absolute quantitation, molecular weight analysis, and report generation. This application supports the iBright CL 1000 and iBright FL 1000 Imaging systems.

ProQuantum

The ProQuantum™ software enables you to analyze ProQuantum™ protein immunoassay results acquired from any qPCR instrument. The analysis features include standard curve qualification with built-in outlier detection, interpolation of unknown samples for quantitation, and group-wise statistical analysis. Step-by-step guidance is provided for preparation of an assay run, including setting up the standard curve, plate layout design, and customized bench instructions.

AnalysisSuite 

This application is for the analysis of dPCR data from the QuantStudio 3D Instrument platform. The software yields absolute Copies/uL and Target/Total results.

Cloud Connect Utility

Cloud Connect Utility is a desktop client for the Connect user to continuously synchronize/upload data to their TFC account and view realtime upload status. CCU lets you securely upload your data files generated from instruments that aren’t cloud-enabled, such as the Applied Biosystems™ StepOne™, StepOnePlus™, 3500XL, QuantStudio6Flex, QuantStudio7Flex, QuantStudio12K Real time PCR, 7900 & 7500 real-time PCR systems, among others. You can also store and backup files, analyze your saved data using TFC’s web-based apps, or securely share your datasets with your colleagues. Windows and Mac versions available.

Education Connect

Education Connect is an online classroom companion supporting LabCoat Live™— the first of its kind, virtual hands-on learning program. The capability provides all of the resources needed for your individualized scientific learning plan. Features include live lecture space for theoretical and data analysis overviews, resource libraries for course lecture notes, protocols, instructional videos, and a discussion board enabling peer-to-peer and participant-to-instructor communication for up to two months after course completion.

Oncomine Reporter

Oncomine Reporter helps you prioritize variants, find the relevant cancer drivers, and create a report that enables contextual investigation of sample-specific variants to understand their use with respect to current labels, guidelines, and global clinical trials. It is a genomic analysis tool developed specifically for further examination of NGS data, enabling streamlined access to a final report in just a few easy steps.

ProcartaPlex Analysis App

The ProcartaPlex Analysis App enables you to analyze ProcartaPlex Multiplex Immunoassay data acquired on Luminex and BioPlex™ instruments. Immediately start your biomarker profiling by easily assigning lot-specific ProcartaPlex assay information to your multiplex data. The intuitive software features 4PL/5PL curve fit optimization, group-wise statistical and heat map analysis. Users can export detailed reports including images for presentations and publications.

QuantiGene Plex Data Analysis

QuantiGene Plex Data Analysis provides differential gene expression analysis on Luminex data files generated using the Invitrogen QuantiGene Plex Assay. Users can review data quality control, assess stability of reference genes, normalize median fluorescence intensity signals to those of reference genes, measure expression of samples individually or in groups, and calculate fold changes of expression. Additionally, users can export data as CHP files for use with the Transcriptome Analysis Console (TAC) Software. Applications include but are not limited to: secondary compound screening in drug discovery, biomarker validation in cancer research, and expression analysis in plants.