RnBeads/DESCRIPTION at master · epigen/RnBeads · 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
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
Package: RnBeads
Title: RnBeads
Description: RnBeads facilitates comprehensive analysis of various types of DNA
    methylation data at the genome scale.
Authors@R: c(
    person("Yassen", "Assenov", email = "assenov@gmail.com",
    role = c("aut")),
    person("Christoph", "Bock", email = "cbock@cemm.at",
    role = c("aut")),
    person("Pavlo", "Lutsik", email = "p.lutsik@dkfz.de",
    role = c("aut")),
    person("Michael", "Scherer", email = "mscherer@mpi-inf.mpg.de",
    role = c("aut")),
    person("Fabian", "Mueller", email = "team@rnbeads.org",
    role = c("aut", "cre")))
Date: 2026-02-17
Version: 2.27.3
Suggests:
    Category,
    GOstats,
    Gviz,
    IlluminaHumanMethylation450kmanifest,
    RPMM,
    RnBeads.hg19,
    RnBeads.mm9,
    RnBeads.hg38,
    XML,
    annotate,
    biomaRt,
    foreach,
    doParallel,
    ggbio,
    isva,
    mclust,
    mgcv,
    minfi,
    nlme,
    org.Hs.eg.db,
    org.Mm.eg.db,
    org.Rn.eg.db,
    quadprog,
    rtracklayer,
    qvalue,
    sva,
    wateRmelon,
    wordcloud,
    qvalue,
    argparse,
    glmnet,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    scales,
    missMethyl,
    impute,
    shiny,
    shinyjs,
    plotrix,
    hexbin,
    RUnit,
    MethylSeekR,
    sesame,
    dplyr
Depends:
    R (>= 3.0.0),
    BiocGenerics,
    S4Vectors (>= 0.9.25),
    GenomicRanges,
    MASS,
    cluster,
    ff,
    fields,
    ggplot2 (>= 0.9.2),
    gplots,
    grid,
    gridExtra,
    limma,
    matrixStats,
    methods,
    illuminaio,
    methylumi,
    plyr,
    reshape2
Imports:
    IRanges
License: GPL-3
biocViews: DNAMethylation, MethylationArray, MethylSeq, Epigenetics,
    QualityControl, Preprocessing, BatchEffect, DifferentialMethylation,
    Sequencing, CpGIsland, ImmunoOncology, TwoChannel, DataImport
Collate:
    'CNV.R'
    'Report-class.R'
    'Report-methods.R'
    'ReportPlot-class.R'
    'ReportPlot-methods.R'
    'RnBDiffMeth-class.R'
    'bigFf.R'
    'RnBSet-class.R'
    'RnBeadSet-class.R'
    'RnBeadRawSet-class.R'
    'RnBeads-package.R'
    'RnBiseqSet-class.R'
    'agePrediction.R'
    'annotations.R'
    'batch.R'
    'batch.quality.R'
    'bmiq.R'
    'cellTypeAdjustment.R'
    'clusterArchitecture.R'
    'clusterArchitectureLSF.R'
    'clusterArchitectureSGE.R'
    'clusterArchitectureSLURM.R'
    'clustering.R'
    'combining.R'
    'computeCluster.R'
    'controlPlots.R'
    'controlPlotsBiSeq.R'
    'dataExport.R'
    'dataImport.R'
    'differentialMethylation.R'
    'differentialVariability.R'
    'enmix.R'
    'enrichment.R'
    'exportGEO.R'
    'filtering.R'
    'filteringSummary.R'
    'genomewide.R'
    'greedycut.R'
    'immune.R'
    'loading.R'
    'logger.R'
    'lolaUtils.R'
    'main.R'
    'normalization.R'
    'normalizationMethods.R'
    'options.R'
    'parallelProcessing.R'
    'plottingUtils.R'
    'profiles.R'
    'qualityControl.R'
    'readGEO.R'
    'regionDescription.R'
    'regionProfiles.R'
    'segmentation.R'
    'sesame.R'
    'sex.R'
    'subSegments.R'
    'sva.R'
    'utilities.R'
    'wbcInference.R'
    'xenomix.R'
RoxygenNote: 7.3.3