SJMack

Steve Mack, PhD

Associate Professor
Division of Allergy, Immunology and BMT UCSF Department of Pediatrics

Overview
Research
Software
Publications
Scientists and Staff

Email
Phone: 510-597-7145

 

Software

Allele Name Translation Tool (ANTT)
The ANTT is a .Net application that translates HLA allele names between IPD-IMGT/HLA Database release versions, as well as user-defined nomenclatures. Described by Mack and Hollenbach. 2010: https://dx.doi.org/10.1111%2Fj.1399-0039.2010.01477.x
Available at: http://igdawg.org/software/antt.html

Global HLA Frequency Map Browser
A web-based browser written in Javascript that allows comparison of HLA allele frequency interpolation maps developed by Solberg et al. 2008: https://dx.doi.org/10.1016/j.humimm.2008.05.001
Available at: http://igdawg.org/software/browser-beta.html

Bridging Immunogenomic Data Analysis Workflow Gaps (BIGDAWG)
BIGDAWG is an R package automates the case-control analysis of highly polymorphic genetic data (e.g., HLA and KIR). Described by Pappas et. al. 2015: https://dx.doi.org/10.1016/j.humimm.2019.01.010 and https://dx.doi.org/10.1016/j.humimm.2019.05.018
Available at: https://cran.r-project.org/package=BIGDAWG

phased or unphased linkage disequilibrium (pould) 
Pould is an R package that calculates four LD measures (D’, Wn, Wa/b and Wb/a) for pairs of genetic loci, allows phase to be estimated via EM methods, or taken as submitted, and generates heat maps of LD values for all locus pairs. Described by Osoegawa et al., 2019a and 2019b: doi:10.1016/j.humimm.2019.01.010 and doi:10.1016/j.humimm.2019.05.018
Available at: https://cran.r-project.org/package=pould

Searching Shared HLA Amino Acid Residue Prevalence (SSHAARP)
SSHAARP generates Solberg-style frequency interpolation maps for user-defined HLA amino acid motifs.
Available at: https://cran.r-project.org/package=SSHAARP

 

Revised: April 29, 2020 4:51 PM

 

© 2005 Children's Hospital Oakland Research Institute
5700 Martin Luther King Jr Way • Oakland, California 94609
Phone 510-450-7600 • Fax 510-450-7910
Site MapDisclaimer