Data Acquisition and Basic Analyses
GeneChip® Command Console® (AGCC)
AGCC is the latest generation of instrument control software for GeneChip systems. The Command Console® software provides an intuitive set of tools for instrument control and data management used in the processing of GeneChip Arrays. Genome Explorations uses the AGCC suite for automated data collection and instrument control with the GeneChip® Fluidics Station 400 and the GeneChip® Scanner 3000. Using the latest in scientific algorithms, the software summarizes probe cell intensity data (CEL file generation) and enables sample/array registration, data management, instrument control, and automatic image gridding for downstream probe-level summarization (CHP file generation) via other Affymetrix software applications or Bioconductor modules. The Command Console® software provides seamless integration with downstream primary analysis applications such as Affymetrix® Expression Console, Axiom Analysis Suite, Genotyping Console, and Transcriptome Analysis Console.
Affymetrix® Expression Console ™ Software
The Expression Console™ provides an intuitive software package allowing for quick and easy intensity normalization, data quality control, and data summarization for any GeneChip array. Using the latest advancements in normalization algorithms, the Expression Console contains convenient, standardized workflows for both gene-level and exon-level analysis. Genome Explorations harnesses the Expression Console to summarize data from thousands of samples, across thousands of genes, hundreds of thousands of exons, and hundreds of thousands of different transcript isoforms. The software provides a convenient, easy-to-use analysis workflow that enables CHP files to be generated from CEL files with minimal effort using standardized approaches tailored by Affymetrix and informed by the latest scientific advancements in genomics. Downstream, the Expression Console provides seamless integration with Affymetrix® Transcription Analysis Console for analysis of Affymetrix transcriptomic microarray solutions.
Affymetrix® Transcriptome Analysis Console (TAC) Software 4.0
TAC 4.0 was developed by Affymetrix to overcome the complexities of identification of differential expression, identification of alternative splicing events, and visualization of complex gene pathway networks, miRNA and target gene interactions, and alternative splicing events. Combined with the comprehensive coverage of Affymetrix high-density microarray solutions, Genome Explorations uses TAC 4.0 software for advancing from raw data to biological results in minutes. Integrating the advanced LIMMA & EventPointer capabilities from Bioconductor, Genome Explorations uses the TAC 4.0 software to provide a basic analysis workflow for performing simple statistical tests for differential expression and splicing events in low-complexity experimental models.
Affymetrix® DMET™ Console
DMET™ Console Analysis Software provides both the flexibility for user-defined reporting as well as comprehensive translation for the most relevant genes. The DMET Plus Solution, which includes arrays, assay, and the DMET Console Analysis Software, provides the broadest coverage, single pharmacogenetic assay. Genome Explorations utilizes the DMET system to enable rapid genetic analysis of the involvement of metabolic pathways in drug metabolism for clinical pharmacogenetic research. Using the DMET system allows us to take one step closer towards the vision of personalized medicine by helping to avoid adverse drug responses, increase treatment efficacy, and provide improved healthcare outcomes.
Chromosome Analysis Suite (ChAS)
Chromosome Analysis Suite is a software offering intuitive and flexible workflow for accurate analysis tailored for cytogenetics. ChAS was developed with input from leading experts and is customized for copy number and cytogenetics research analysis and reporting. ChAS allows for the summarization of chromosomal aberrations across the genome. Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss/absence of heterozygosity (LOH/AOH). Combined with expression data, we can integrate copy number data with Concurrent Molecular Analysis Profiling (CoMAP™). In addition, ChAS utilizes the latest human genome build (Hg38) to provide the most up-to-date ONIM, DGV, Ensembl, ClinVar, and RefSeq annotations.