A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).

Provides SNP array data from different types of
    copy-number regions. These regions were identified manually by the authors
    of the package and may be used to generate realistic data sets with known
    truth.

Archimax copulas are mixture of Archimedean and EV copulas. The package provides definitions of several parametric families of generator and dependence function, computes CDF and PDF, estimates parameters, tests for goodness of fit, generates random sample and checks copula properties for custom constructs. In 2-dimensional case explicit formulas for density are used, contrary to higher dimensions when all derivatives are linearly approximated. Several non-archimax families (normal, FGM, Plackett) are provided as well.

Exclusion-based parentage assignment is essential for studies in biodiversity conservation and breeding programs - Kang Huang, Rui Mi, Derek W Dunn, Tongcheng Wang, Baoguo Li, (2018), <doi:10.1534/genetics.118.301592>. The tool compares multilocus genotype data of potential parents and offspring, identifying likely parentage relationships while accounting for genotyping errors, missing data, and duplicate genotypes. 'acoRn' includes two algorithms: one generates synthetic genotype data based on user-defined parameters, while the other analyzes existing genotype data to identify parentage patterns. The package is versatile, applicable to diverse organisms, and offers clear visual outputs, making it a valuable resource for researchers.

Make acoustic cues to use with the R packages 'ndl' or 'ndl2'. The package implements functions used
              in the PLoS ONE paper:
              Denis Arnold, Fabian Tomaschek, Konstantin Sering, Florence Lopez, and R. Harald Baayen (2017).
              Words from spontaneous conversational speech can be recognized with human-like accuracy by 
              an error-driven learning algorithm that discriminates between meanings straight from smart 
              acoustic features, bypassing the phoneme as recognition unit.  PLoS ONE 12(4):e0174623
              <doi:10.1371/journal.pone.0174623>
              More details can be found in the paper and the supplement.
              'ndl' is available on CRAN. 'ndl2' is available by request from <konstantin.sering@uni-tuebingen.de>.