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Genomic and RNA Profiling Core Facility

Houston, Texas

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Genomic and RNA Profiling Core
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Data Analysis - Alternative Software


GeneSpring

Affymetrix data files (.cel, .chp, .txt) and Agilent data files (.txt) can be imported into GeneSpring. If you are interested in obtaining access to GeneSpring for analysis purposes, please contact the Computational and Integrative Bioinformatics Research Center.

Agilent's Cytogenomics software is a complete CGH and CGH+SNP microarray data analysis and data reporting solution to streamline the day-to-day cytogenetic sample analysis research workflow. This software license is free-of-charge for one year.

Learn more about Agilent's Cytogenomics software here.

dChip

dChip Software (DNA-Chip Analyzer) is a free program designed for statistical analysis of Affymetrix GeneChips®.

Two helpful references on dChip:

Utilize Affymetrix' GeneChip® Command Console (AGCC) and Transcriptome Analysis Console (TAC) softwares to analyze microarray data. Affymetrix also provides information and help in selecting the correct tools to analyze GeneChip® data on the Compatible Software page on the Affymetrix website.

BIOConductor

BIOConductor (RNA Analysis) is another free program for analyzing array data. Please contact the GARP if you, would like your data run through BIOConductor or would like more information on this free software.

Partek

Partek Genomics Suite (Partek GS) can be used to analyze data generated from microarray and sequencing projects. It can import and analyze raw and processed data from all major chip platforms, and can seamlessly import data from .CEL, .CHP, .CNT (CNAT), .MSK, metaprobeset files, and plain text file formats from one color and two-color microarrays. Partek GS also automatically provides links to NetAffx, UCSC Genome Browser, IGB, and other internet databases.

In addition, GARP has a a Partek license on a dedicated workstation for users interested in performing independent data analysis of microarray and sequencing projects. Please contact GARP to make arranges for Partek Workstation use.

Array Cards can be analyzed using Life Technologies' ViiA7, DataAssist or ExpressionSuite software. All three softwares are free, however, you will need a registration code for the ViiA7 software, which can be attained by contacting GARP. GARP will supply the registration code with each array card request in the note section of each MAID request.

Both ViiA7 and DataAssist allow users to analyze qPCR array card data files, however, ViiA7 software allows users to additionally make adjustments to baselines and thresholds, while DataAssist and ExpressionSuite do not. Please visit the Life Technologies website for more information on these softwares. Download these softwares here: ViiA7, DataAssist and ExpressionSuite.

Note: Mac Users will need to remove the ".txt" suffix automatically added to the data file after downloading in order for ViiA7 software to recognize the file format.

NanoString® Technologies recommends data generated using the nCounter® Gene Expression Assays be analyzed using NanoString's nSolver® Data Analysis Software. Users may download the nSolver Data Analysis Software on NanoString's website for free but will be required to register and sign-in to NanoString's full-access site in order to complete the free download. Additionally, users may access user manuals and other files from the full-access site. Please note: nSolver® Analysis Software is available in both Windows and Mac versions. In order to begin analysis, the RCC (data output file) and RLF (Reporter Library File) will need to be imported into the software. GARP sends these two files to users upon completion of NanoString Requests.

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