Extracts growth, survival, and local neighborhood density 
  information from repeated, fine-scale maps of organism occurrence. Further 
  information about this package can be found in our journal article, 
  "plantTracker: An R package to translate maps of plant occurrence into 
  demographic data" published in 2022 in Methods in Ecology and Evolution 
  (Stears, et al., 2022) <doi:10.1111/2041-210X.13950>.

Estimation, prediction, thresholding, transformation, and plotting for partially linear additive quantile regression.  Intuitive functions for fitting and plotting partially linear additive quantile regression models.  Uses and works with functions from the 'quantreg' package.

Contains tools for supervised analyses of incomplete, overlapping
  multiomics datasets. Applies partial least squares in multiple steps to find
  models that predict survival outcomes. See Yamaguchi et al. (2023)
  <doi:10.1101/2023.03.10.532096>.

Aims at detecting single nucleotide variation
    (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used
    as a surrogate marker for tumor, at each base position of an Next Generation
    Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele
    frequency at each position to the measured PER in control samples.

Aims at detecting single nucleotide variation
    (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used
    as a surrogate marker for tumor, at each base position of an Next Generation
    Sequencing (NGS) analysis using barcoding. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.
    This package has been used for Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund N\o{o}rdgaard (2022) <https://www.nature.com/articles/s41598-022-09698-5>.

Contains functions developed to combine the results of querying a plasmid database using
    short-read sequence typing with the results of a blast analysis against the query results.