List of Software

  1. OmicShare
  2. Association Tests for Annotated Variants (ATAV)
  3. SequenceVariantAnalyzer (SVA)
  4. Statistical Analysis of Antigen Receptor Spectratype Data
  1. OmicShare [top]
  2. OmicShare is a collaborative work environment that enables users to easily store, manage and share all types of instrumental and analytical data files for project management in biomedical research.  It facilitates research collaboration and reduces the risk of data loss.  OmicShare has a user friendly interface accessed through an Internet browser.  Data files are uploaded to the system underlying a robust database (The database can be any one of the relational databases, such as Oracle, MySQL, PostgreSQL, etc.) by selecting, coping, or simple drag-and-drop files.  OmicShare allows users to upload/download multiple subfolders and files by a simple click.  Folders or files can be granted different permissions to other collaborators by the data supplier or system administrator.  OmicShare allows users to share files with collaborators quickly, easily, and professionally.   Users can securely and quickly navigate to the projects in which they are involved to communicate with other collaborators inside and outside their organizations, upload/download single or multiple data file(s) by one click, as well as download analyses.  Click here to evalute the software.
  3. Association Tests for Annotated Variants (ATAV) [top]
  4. ATAV is a statistical toolset that is designed to detect complex disease-associated rare genetic variants by performing association analysis, trio analysis, and/or linkage analysis on whole-genome or whole-exome sequencing data.  Click here for more details.
  5. SequenceVariantAnalyzer (SVA) [top]
  6. SVA is a computer software project designed to annotate and visualize the genetic variants identified through next-generation sequencing studies, including whole-genome and whole-exome sequencing studies. It is a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. The annotated variants can be exported to a separate statistical tool, for example ATAV.  Click here for more details.
  7. Statistical Analysis of Antigen Receptor Spectratype Data [top]
  8. Spectratype analysis (SpA) is a method used in clinical and basic immunological settings in which antigen receptor length diversity is assessed as a surrogate for functional diversity. We have developed the statistical methods appropriate for the comparison of multiple different spectratypes in a variety of ways. The fundamental statistic for these comparisons and statistical tests is the completeness, an information-theoretic quantity that arises naturally in the statistical derivations. The completeness is closely related to the entropy as a measure of the diversity of the antigen receptor repertoire and serves as a sensitive and objective measure of the state of the repertoire. Several of the statistical tests based on the completeness are performed automatically upon data submission, and additional tests are available to the user online through SpA. Specialized statistical tools, developed for hypothesis testing and modeling for multiple spectratypes, are also available through the SpA interface. In addition to the specific procedures provided by SpA, the powerful, general-purpose data analysis package R is integrated into SpA system for more specialized procedures (Bioinformatics, 2005, 21, 3394-3400; Bioinformatics, 2005, 21, 3697-3699). SpA is used both on campus and throughout the world.