Software

Last updated 5 April 2022

  1. qqconf: Q-Q plots with simultaneous testing regions; calculations for equal local levels global testing method

    New! R package Version 1.2.3 released March 29, 2022 github CRAN

    E. Weine, M. S. McPeek and M. Abney "Application of Equal Local Levels to Improve Q-Q Plot Testing Bands with R Package qqconf" (2022) arXiv:2111.15082

  2. CARAT: Case-control association analysis accounting for population structure and covariates

    Version 1.3 released July 23, 2020

  3. ATOMM: Mixed effects model for mapping a two-organism phenotype to a pair of genomes simultaneously

    Version 1.0 released June 18, 2018

    M. Wang, F. Roux, C. Bartoli, C. H.-Chauveau, C. Meyer, H. Lee, D. Roby, M. S. McPeek, and J. Bergelson "Two-way mixed-effects methods for joint association mapping analysis using both host and pathogen genomes" (2018) PNAS vol. 115 no. 24 E5440-E5449

  4. MONSTER: robust SNP-set association testing of a quantitative trait in samples with related individuals

    Version 1.3 released December 17, 2016

    Jiang D., McPeek M. S. "Robust rare variant association testing for quantitative traits in samples with related individuals" (2014) Genetic Epidemiology 38:10-20.

  5. G-STRATEGY: Optimal selection of individuals for sequencing in genetic association studies, based on phenotypes, covariates and pedigrees

    Version 1.0 released November 18, 2016

    Wang M., Jakobsdottir J., Smith A. V., McPeek M. S. "G-STRATEGY: Optimal selection of individuals for sequencing in genetic association studies" (2016) Genetic Epidemiology 40:446-460.

  6. CERAMIC: Mixed-Model Association Analysis of Binary Traits in Samples with Related Individuals

    Version 1.0 released October 23, 2016

    Zhong S., Jiang D., McPeek M. S. (2016). Case-Control Association Testing in Samples with Related Individuals Based on Retrospective Mixed Model Analysis with Adjustment for Covariates. PLoS Genetics 12(10):.e1006329. doi:10.1371/journal.pgen.1006329.

  7. MASTOR: Association testing of a quantitative trait in samples with related individuals, allowing for covariates and missing data

    Version 0.7 released December 1, 2015

  8. ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure

    Version 2.0 released November 2013

    Thornton T., McPeek M. S. "ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure" (2010) American Journal of Human Genetics 86:172-184.

  9. MQLS_XM: Autosomal and X-chromosome association testing of a binary trait in case-control samples with related individuals

    Version 1.0 released July 2012

  10. FORMAT_PED_PHENO: Software for formatting a pedigree/phenotype information file

    Version 1.0 released July 2012

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

    Version 1.5 released March 2011

    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

  12. IQLS: Haplotype analysis for case-control samples with related individuals

    Version 1.2 of IQLS released March 2011

    Wang Z., McPeek M. S. "An incomplete-data quasi-likelihood approach to haplotype-based genetic association studies on related individuals" (2009) J. Am. Stat. Assoc. 104:1251-1260.

  13. ATRIUM: Testing untyped SNPs in case-control association studies with related individuals

    Version 1.0 released October 2009

    Wang Z., McPeek M. S. "ATRIUM: testing untyped SNPs in case-control association studies with related individuals" (2009) American Journal of Human Genetics 85:667-678

  14. KinInbcoefX: Calculation of X-chromosome kinship coefficients

    Version 2.0 of KinInbcoefX released May 2009

  15. KinInbcoef: Calculation of kinship and inbreeding coefficients

    Version 1.1 of KinInbcoef released June 2009

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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