OmicsSuite

OmicsSuite provides integrated analysis and processing of multi-omics and mass spectrometry data to support biological interpretation of high-throughput sequencing from Illumina, PacBio and 10X Genomics platforms and gas/liquid chromatography-mass spectrometry experiments.

Key Features:

• Multi-omics scope: Comprises 175 sub-applications organized into 12 categories: Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation.
• Supported technologies: Supports data originating from Illumina, PacBio, 10X Genomics and gas/liquid chromatography-mass spectrometry.
• Data format support: Direct reading of FastA, FastQ, Mutation Annotation Format (MAF), mzML, Matrix, and HDF5 files.
• Computational implementation: Implemented using Java 11 with application components developed using BioJava.
• R ecosystem integration: Leverages over 300 packages from R CRAN and Bioconductor for analytical functionality.
• Parameterization: Exposes more than 3,000 adjustable parameter interfaces to configure analyses.
• Pipeline capabilities: Provides pipeline analysis functions and efficient data transfer directions for multi-omics workflows.
• Output generation: Generates images and tables for downstream analysis and reporting.

Scientific Applications:

• Horticultural plant breeding: Supports multi-omics workflows applicable to breeding studies in horticultural species.
• Molecular mechanism studies in plants: Enables integration of genomics, transcriptomics, proteomics and metabolomics for plant molecular mechanism investigations.
• Multi-omics integration: Facilitates step-by-step multi-omics analyses of large-scale sequencing and mass spectrometry datasets.
• Domain-specific analyses: Provides analytical capabilities relevant to Clinical, Microorganism and Single Cell omics investigations.

Methodology:

Implemented in Java 11; applications developed using BioJava; leverages over 300 R CRAN and Bioconductor packages; reads FastA, FastQ, Mutation Annotation Format (MAF), mzML, Matrix and HDF5 formats; comprises 175 sub-applications in 12 categories; exposes >3,000 adjustable parameter interfaces; and provides pipeline analysis functions and efficient data transfer directions.