MetaboDynamics/DESCRIPTION at RELEASE_3_22 · KatjaDanielzik/MetaboDynamics · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
Package: MetaboDynamics
Title: Bayesian analysis of longitudinal metabolomics data
Version: 2.0.2
Authors@R:
  c(person(given="Katja",family= "Danielzik", email="katja.danielzik@uni-due.de",
           role = c("aut", "cre"),
           comment=c(ORCID="0009-0007-5021-6212")),
    person(given="Simo",family="Kitanovski",role="ctb",
           comment=c(ORCID="0000-0003-2909-5376")),
    person(given="Johann",family="Matschke",role="ctb",
           comment=c(ORCID="0000-0003-4878-8741")),
    person(given="Daniel",family="Hoffmann",role="ctb",
           comment=c(ORCID="0000-0003-2973-7869")))
URL: https://github.com/KatjaDanielzik/MetaboDynamics
BugReports: https://github.com/KatjaDanielzik/MetaboDynamics/issues
Description: MetaboDynamics is an R-package that provides a framework of
  probabilistic models to analyze longitudinal metabolomics data. It enables
  robust estimation of mean concentrations despite varying spread between
  timepoints and reports differences between timepoints as well as metabolite
  specific dynamics profiles that can be used for identifying "dynamics clusters"
  of metabolites of similar dynamics. Provides probabilistic over-representation
  analysis of KEGG functional modules and pathways as well as comparison between
  clusters of different experimental conditions.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests:
  knitr,
  rmarkdown,
  BiocStyle,
  testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports:
  dplyr,
  ggplot2,
  KEGGREST,
  methods,
  Rcpp (>= 0.12.0),
  RcppParallel (>= 5.0.1),
  rstan (>= 2.18.1),
  rstantools (>= 2.4.0),
  S4Vectors,
  stringr,
  SummarizedExperiment,
  tidyr,
  dynamicTreeCut,
  rlang,
  ape,
  ggtree,
  patchwork
VignetteBuilder: knitr
Depends:
  R (>= 4.4.0)
LazyData: false
LinkingTo:
  BH (>= 1.66.0),
  Rcpp (>= 0.12.0),
  RcppEigen (>= 0.3.3.3.0),
  RcppParallel (>= 5.0.1),
  rstan (>= 2.18.1),
  StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
biocViews: Software,Metabolomics,Bayesian,FunctionalPrediction,MultipleComparison,KEGG,Pathways,TimeCourse, Clustering
Biarch: true