The new (dQTG.seq1 and dQTG.seq2) and existing (SmoothLOD, G', deltaSNP and ED) bulked segregant analysis methods are used to identify various types of quantitative trait loci for complex traits via extreme phenotype individuals in bi-parental segregation populations (F2, backcross, doubled haploid and recombinant inbred line). The numbers of marker alleles in extreme low and high pools are used in existing methods to identify trait-related genes, while the numbers of marker alleles and genotypes in extreme low and high pools are used in the new methods to construct a new statistic Gw for identifying trait-related genes. dQTG-seq2 is feasible to identify extremely over-dominant and small-effect genes in F2.
BB, data.table, doParallel, openxlsx, qtl, stringr, writexl,
parallel,foreach

Functions for direct surrogate variable analysis, which can identify hidden factors in high-dimensional biomedical data.

Multi-Way Spherical Clustering via Degree-Corrected Tensor Block
Models
c(person(given = "Jiaxin",family = "Hu",role = c("aut", "cre","cph"),email = "jhu267@wisc.edu"), person(given = "Miaoyan",family = "Wang",role = c("aut", "cph"),email = "miaoyan.wang@wisc.edu"))
Implement weighted higher-order initialization and angle-based iteration for multi-way spherical clustering under degree-corrected tensor block model.
Jiaxin Hu [aut, cre, cph],
Miaoyan Wang [aut, cph]

Damped Anderson Acceleration with Epsilon Monotonicity for
Accelerating EM-Like Monotone Algorithms
c(person("Nicholas", "Henderson", email = "nhender5@jhmi.edu", role = "cre"), person("Ravi", "Varadhan", email = "ravi.varadhan@jhu.edu", role = "aut"))
Implements the DAAREM method for accelerating the convergence of slow, monotone sequences from smooth, fixed-point iterations such as the EM algorithm. For further details about the DAAREM method. see Henderson, N.C. and Varadhan, R. (2018) <arXiv:1803.06673>.
Nicholas Henderson [cre],
Ravi Varadhan [aut]

c(person("Nicholas", "Henderson", email = "nhender5@jhmi.edu", role = c("cre", "aut")), person("Ravi", "Varadhan", email = "ravi.varadhan@jhu.edu", role = "aut"))
Nicholas Henderson [cre, aut],
Ravi Varadhan [aut]