Genome wide analysis of RNA Polymerase II-based ChIP Seq data.
Martial Sankar, supervised by Marco Mendoza and Hinrich Gronenmeyer
Polyphemus is able to combine signal intensity (count) profiles, with significant peak annotations in order to identify coding regions of interest for the comparative analysis or two or more samples. The algorithm (i) identifies significant coding regions, (ii) performs normalization, (iii) compares several profiles and (iv) provides matrix output suitable for further clustering analysis.
IRanges, zoo, RUnit, parallel, R.utils, limma

Helper Functions for Orthogonal Polynomials
person("Tristan", "Mahr", email = "tristan.mahr@gmail.com", role = c("aut", "cre"))
Tools for reshaping, plotting, and manipulating matrices of orthogonal polynomials.
testthat, knitr, rmarkdown, lme4, splines

person(
given = "Tristan",
family = "Mahr",
role = c("aut", "cre"),
email = "tristan.mahr@wisc.edu",
comment = c(ORCID = "0000-0002-8890-5116")
)

QTL Analysis in Autopolyploid Bi-Parental F1 Populations
c(person("Peter","Bourke", email = "pbourkey@gmail.com", role = c("aut","cre")),
person("Christine","Hackett", role = "aut"),
person("Chris","Maliepaard", role = "ctb"),
person("Geert","van Geest", role = "aut"),
person("Roeland","Voorrips", role = "ctb"),
person("Johan","Willemsen", role = "ctb"))
Quantitative trait loci (QTL) analysis in polyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
The methods have been largely described in the dissertation of P.M. Bourke in 2018 <doi:10.18174/444415>.
abind, doParallel, foreach, Hmisc, knitr, nlme, RColorBrewer,
Rcpp (>= 0.12.19), reshape2, rmarkdown
Peter Bourke [aut, cre],
Christine Hackett [aut],
Chris Maliepaard [ctb],
Geert van Geest [aut],
Roeland Voorrips [ctb],
Johan Willemsen [ctb]

Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in
autopolyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
The methods have been largely described in the dissertation of P.M. Bourke in 2018 <doi:10.18174/444415>.
abind, doParallel, foreach, Hmisc, knitr, nlme, RColorBrewer,
Rcpp (>= 0.12.19), reshape2