Software

Last updated 8 June 2009

  1. MQLS: More powerful case-control association test of a binary trait in samples that contain related individuals

    Thornton T., McPeek M. S. "Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test" (2007) American Journal of Human Genetics 81:321-337

  2. KinInbcoefX: Calculation of X-chromosome kinship coefficients

    New: version 2.0 of KinInbcoefX just released!

  3. KinInbcoef: Calculation of kinship and inbreeding coefficients

    New: version 1.1 of KinInbcoef just released!

  4. PREST (Pedigree RElationship Statistical Test) --- detection of misspecified relationships in pedigrees by use of genome screen data

    Sun L., Wilder K., McPeek M. S. "Enhanced pedigree error detection" (2002) Human Heredity vol 54, pp. 99-110
    McPeek, M. S., Sun L. "Statistical tests for detection of misspecified relationships using genome screen data" (2000) American Journal of Human Genetics vol 66, pp. 1076-1094
    Sun L., Abney M., McPeek M. S. "Detection of misspecified relationships in inbred and outbred pedigrees" (2001) Genetic Epidemiology vol 21, pp. S36-S41

  5. STEPC (Statistical Explanation for Positional Cloning) --- confidence sets of polymorphisms that can explain a linkage result for a qualitative trait

    Sun L., Cox N. J., McPeek M. S. "A statistical method for identification of polymorphisms that explain a linkage result" (2002) American Journal of Human Genetics vol 70, pp. 399-411

  6. DHSMAP (Decay of Haplotype Sharing MAPping Software) --- fine-mapping of qualitative traits by use of linkage disequilibrium

    McPeek, M. S., Strahs, A. "Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping" (1999) American Journal of Human Genetics vol 65, pp. 858-875
    Strahs A., McPeek M.S. "Multipoint fine-scale linkage disequilibrium mapping: importance of modeling background LD" (2003) IMS Lecture Notes Monograph Series, Volume 40 Science and Statistics: A Festschrift for Terry Speed, Darlene R. Goldstein, ed., pp. 343-366

  7. PVM version of DHS Map ---parallelized version of DHSMAP

    McPeek, M. S., Strahs, A. "Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping" (1999) American Journal of Human Genetics vol 65, pp. 858-875
    Strahs A., McPeek M.S. "Multipoint fine-scale linkage disequilibrium mapping: importance of modeling background LD" (2003) IMS Lecture Notes Monograph Series, Volume 40 Science and Statistics: A Festschrift for Terry Speed, Darlene R. Goldstein, ed., pp. 343-366

  8. DHS-R (Decay of Haplotype Sharing for related individuals) --- A version of DHSMAP that allows related individuals

    Zhang J., Schneider D., Ober C., McPeek M. S. "Multilocus linkage disequilibrium mapping by the decay of haplotype sharing with samples of related individuals" (2005) Genetic Epidemiology, vol. 29, pp. 128-140

  9. CC-QLS (Association testing in case-control samples that include related individuals with known genealogy)

    Bourgain C., Hoffjan S., Nicolae R., Newman D., Steiner L., Walker K., Reynolds R., Ober C., McPeek M. S. "Novel case-control test in a founder population identifies P-selectin as an atopy susceptibility locus" (2003) American Journal of Human Genetics vol 73, pp. 612-626

  10. SPERMSEG --- analysis of segregation distortion in single sperm data

    McPeek M. S., "SPERMSEG: analysis of segregation distortion in single sperm data" (1999) American Journal of Human Genetics vol 65, pp. 1195-1197
    Leeflang, E., McPeek, M. S., Arnheim, N. "Analysis of meiotic segregation using single-sperm typing: meiotic drive at the myotonic dystrophy locus" (1996) American Journal of Human Genetics vol. 59, pp. 896-904.
    Grewal, R. P., Cancel G., Leeflang E. P., Duerr A., McPeek M. S., Draghinas D., Xiang Y., Stevanin G., Alnot M.-O., Brice A., Arnheim N. "French Machado-Joseph Disease patients do not exhibit gametic segregation distortion: a sperm typing analysis" (1999) Human Molecular Genetics vol 8, pp. 1779-1784
    Girardet A., McPeek M. S., Leeflang E. P., Munier F., Arnheim N., Claustres M., Pellestor F. "Meiotic segregation analysis of RB1 alleles in retinoblastoma pedigrees by use of single-sperm typing" (2000) American Journal of Human Genetics vol 66, pp. 167-175