Order-Restricted Inference for Microarray Experiments
Dan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
The package offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
xtable, Biobase, affy, ff(>= 2.0.0), tcltk

Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.

Retrieve Data using the Max Plank Institute 'IsoMemo' API
c(
person("Jianyin", "Roachell", ,"jianyin.roachell@inwt-statistics.de","cre"),
person("Andreas", "Neudecker", , "andreas.neudecker@inwt-statistics.de","aut"),
person("Ricardo", "Fernandes", , "fernandes@shh.mpg.de","aut")
)
API wrapper that contains functions to retrieve data from the 'IsoMemo' partnership databases. Web services for API: <https://isomemodb.com/api/v1/iso-data>.
Jianyin Roachell [cre],
Andreas Neudecker [aut],
Ricardo Fernandes [aut]

Mateusz Krzysztof Łącki and Michał Startek
IsoSpec is a fine structure calculator used for obtaining the most
probable masses of a chemical compound given the frequencies of the composing
isotopes and their masses. It finds the smallest set of isotopologues with
a given probability. The probability is assumed to be that of the product of
multinomial distributions, each corresponding to one particular element and
parametrized by the frequencies of finding these elements in nature. These
numbers are supplied by IUPAC - the International Union of Pure and Applied
Chemistry.