A client for interacting with 'magma', the data warehouse of the
    'UCSF Data Library'. 'magmaR' includes functions for querying and
    downloading data from 'magma', in order to enable working with such data in
    R, as well as for uploading local data to 'magma'.

Correlates variation within the meta-genome to target species
    phenotype variations in meta-genome with association studies. Follows
    the pipeline described in Chaston, J.M. et al. (2014) <doi:10.1128/mBio.01631-14>.

Implements an interface to the legacy Fortran code from O'Connell and Dobson (1984) <DOI:10.2307/2531148>. Implements Fortran 77 code for the methods developed by Schouten (1982) <DOI:10.1111/j.1467-9574.1982.tb00774.x>. Includes estimates of average agreement for each observer and average agreement for each subject.

Provides a mechanism for chaining commands with a new
    forward-pipe operator, %>%. This operator will forward a value, or the
    result of an expression, into the next function call/expression.
    There is flexible support for the type of right-hand side expressions.
    For more information, see package vignette.  To quote Rene Magritte,
    "Ceci n'est pas un pipe."

Provides a comprehensive graphical user interface for analysis of Affymetrix, Agilent, Illumina, Nimblegen and other microarray data. It can perform miscellaneous tasks such as gene set enrichment and test analyses, identifying gene symbols and building co-expression network. It can also estimate sample size for atleast two-fold expression change. The current version is its slenderized form for compatable and flexible implementation.

The current version (0.3.0) streamlines the underlying code, adds a feasibility check to 'maicWt' and 'maxessWt', extends 'exmWt.2ipd' with options 'target.ipd' and 'method' for one-sided MAIC weighting between two IPDs, and adds 'wtTrtDiff' for the weighted treatment-effect difference with a Wald confidence interval based on Section 5 of Glimm & Yau (2026). The second version (0.2.0) contains implementation for exact matching which is an alternative to propensity score matching (see Glimm & Yau (2026) <doi:10.1080/19466315.2025.2507378>). The initial version (0.1.2) contains a collection of easy-to-implement tools for checking whether a MAIC can be conducted, as well as an alternative way of calculating weights (see Glimm & Yau (2022) <doi:10.1002/pst.2210>.)