Qlucore Omics Explorer

Category Genomics>Gene Expression Analysis/Profiling/Tools and Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract Qlucore Omics Explorer is a next-generation bioinformatics software program that delivers immediate results.

Using Qlucore Omics Explorer (OE), you can drastically shorten analysis time and add more creativity to your research, thanks to stunning 3D graphics, a point and click user interface, and state of the art statistical analysis.

Quickly analyze and explore data sets such as:

1) Gene expression: microarrays, real-time PCR;

2) MicroRNA: microarrays, real-time PCR;

3) DNA methylation: microarrays;

4) Protein expression: microarrays, antibody arrays, 2-D gels, LC-MS; and

5) Any multivariate data of size up to 1,500 x 50,000 or 150 x 500,000.

OE data analysis software will support the unveiling of important new discoveries as it will allow the actual researchers -- the people with the most biological insight -- to study important data and to look for patterns and structures, without needing to be a statistics or computer expert.

OE data analysis software is very easy to use, and the user is always provided with instant feedback.

Qlucore Omics Explorer enables researchers to analyze and explore extremely large data sets (containing up to more than 100 million data samples) on a regular PC or Mac.

OE data analysis software takes full advantage of all annotations and other links that are connected with the data being studied, as well as a number of advanced statistical functions such as false discovery rates (FDR), f-tests, ANOVA and p-values.

All results are instantly visualized in any of the many plot types.

Plot types such as heat-map and Principal Component Analysis (PCA) are supported. The user can work with any number of synchronized plot types in order to analyze the data from several angles, at the same time.

The current user base spans a broad range of professions, from bioinformaticians, biologists, statisticians and chemists to medical doctors, students and professors.

Qlucore Omics Explorer 2.2 feature overview --

1) Qlucore Omics Explorer (OE) allows very fast data analysis and visualization.

2) OE works in full real time with 3D presentation of all data.

3) OE is unique in how advanced statistical analysis is combined with instant visualization.

4) OE provides simple workflows for mRNA, miRNA data and DNA Methylated data. Including the normalization of Agilent data.

5) With OE you can directly download data from Gene Expression Omnibus (GEO) to compare your findings with published material.

6) OE supports the user to explore the data by changing filters and parameters with only one mouse click.

7) OE support hierarchical clustering and heatmap plots as well as Dynamic Principal Component Analysis (PCA) and all plots are updated instantly.

8) OE only requires a normal PC to handle huge data sets (more than 100 million entries) in real time.

Products Overall features/capabilities include:

Main Functionality --

1) Generate results with false discovery rates (q-value), fold change and p-values;

2) Analyze and explore data set(s) with a combination of visualization and intuitive filters;

3) Perform hierarchical clustering and generate dynamic heat-map plots;

4) Instantly create PCA plots of large data sets on an ordinary PC;

5) Use any of several methods, Hierarchical clustering, PCA, ISOMAP and or graphs to better understand data;

6) Download data from Gene Expression Omnibus (GEO) to compare your own results with published material.

7) Easily work with paired data;

8) Remove unwanted dependencies such as artifacts and outliers;

9) Use set operations on lists;

10) Drill down into you data set by selecting which part of the data to analyze and combine the data with annotations;

11) Benefit from the streamlined workflows for Affymetrix gene expression microarray and Agilent miRNA data;

12) Change parameters at any time with a single mouse click, and automatically get an updated plot immediately (in less than 0.1s);

13) A simple and intuitive user interface; and

14) Keep track of your work with the advanced global log and restore function.

Output --

1) High quality 3-D graphics;

2) Four (4) plot types: Heat-map, sample PCA, variable PCA and scatter plot;

3) Data table view;

4) Color legend window. It explains the colors and scales in the active plot. Can be exported with a plot;

5) Plot both samples and variables;

6) Synchronized plots;

7) Variable lists with p-values, fold change and FDR (q-values) values;

8) Plot arbitrary principal components;

9) Color the samples and the variables through different methods;

10) Label the samples and the variables through different methods; and

11) Present multiple scatter plots in one view.

Editing of data --

1) Interactive editing of sample annotations;

2) Interactive editing of variable lists.

Selection --

1) Work with subsets of samples and variables;

2) Select samples based on clinical variables and other annotations;

3) Select variables based on variance, F-test (ANOVA), t-test, rank correlation, correlation coefficients, annotation text searches and imported variable lists (such as pathways);

4) Select variables based on linear or cubic regression; and

5) Study part of the data set based on imported variable lists (such as pathways).

Variable lists --

1) Automatic variable list for all active variables;

2) Automatic variable list for Search results; and

3) Set operations on variable lists.

Verification --

1) Get direct feedback on p-values and q-values during variable selection;

2) Verify results by redoing the analysis with permuted sample annotations or with random numbers;

3) Verify results through remove-one-at-a-time cross validation or several at the time of cross validation; and

4) Continuous update on captured variance in PCA plot.

Clusters and Networks --

1) Visualize sample clusters by connecting each sample with its nearest neighbors; and

2) Visualize variable clusters by connecting correlated variables.

Import --

1) Data files of .gedata format (normal or transposed);

2) Data files of .txt format (one variable identifier column and one sample identifier row). Called Simple text files;

3) Compact Text files (*.txt or *.csv);

4) Data (GDS and GSE) from Gene Expression Omnibus (GEO). Direct download;

5) GEO soft files (*.soft and *.soft.gz);

6) GEO Series Matrix (*.txt and *.txt.gz);

7) Agilent GeneView files (*.txt) for miRNA data;

8) Agilent Text Files (*.txt)

9) Variable lists;

10) Annotation files;

11) Direct NetAffx import;

12) Affymetrix CHP and ARR files; and

13) Log files.

Export --

1) Still images (plots) including a legend plot. It can be done either in automatic mode or in manual mode. In the manual mode the user can freely select the plot size;

2) Data files;

3) Variable lists (with annotations and data, if so preferred);

4) Videos;

5) Log files; and

6) Correlation and co-variance matrixes.

Other --

1) Missing value reconstruction (two versions);

2) Variable normalization;

3) Multi-dimensional rescaling;

4) ISOMAP;

5) Take logarithm of data; and

6) Simplified Affymetrix annotations.

Manufacturer offers two (2) licensing models for OE --

1) Single user, single computer licenses: A single user, single computer license gives one named user the right to use the software on one computer. The software will be locked to this computer. The license is valid for one year and includes support and upgrades.

2) Network licenses: A network license allows a certain number of concurrent users on a local area network. Any person connected to the network can use the software, as long as the maximal number of concurrent users is Not exceeded. Network licenses are available for five or more concurrent users.

A user can “check out” a license and use the software when Not connected to the network. The license is valid for one year and includes support and upgrades.

Note: In addition to the licensing models above there are also special licenses for Academia.

System Requirements

Qlucore Omics Explorer is available in both a 32 bit and a 64 bit version.

Omics Explorer requires:

Omics Explorer takes full advantage of processors with multiple cores and computers with multiple processors.

For users of Mac computers a virtual Windows solution works well.

Manufacturer

Manufacturer Web Site Qlucore Omics Explorer

Price Contact manufacturer.

G6G Abstract Number 20120R

G6G Manufacturer Number 102235