ChIPbinner/DESCRIPTION at main · padilr1/ChIPbinner · 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
Package: ChIPbinner
Title: Analysis of ChIP-Seq or CUT&RUN/TAG data in binned windows for broad histone marks
Version: 0.99.2
Authors@R:
    c(person(given="Reinnier",family="Padilla",email="reinnier.padilla@mail.mcgill.ca", role = c("aut","cre"),
           comment = c(ORCID = "0009-0005-5646-5450")),
           person(given="Eric", family="Bareke", email="eric.bareke@mcgill.ca", role="ctb"),
           person(given="Bo", family="Hu", email="frank.hu@mail.mcgill.ca", role="ctb"),
           person(given="Jacek", family="Majewski", email="jacek.majewski@mcgill.ca", role=c("aut", "ctb")))
Description: A suite of tools for analyzing ChIP-Seq or CUT&RUN/TAG data that has been binned in uniform windows.
  ChIPbinner provides users with functionalities for signal normalization and combining replicates,
  alongside visualization tools for exploratory analysis, including genic/intergenic scatterplots, principal component analysis and correlation plots.
  Finally, it allows users to identify clusters of similarly-behaving bins, perform differential bin analysis and statistically assess their overlap with specific classes of annotated regions.
License: GPL (>= 3) + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports:
    ggplot2,
    dplyr,
    GenomicRanges,
    IRanges,
    rtracklayer,
    data.table,
    patchwork,
    isoband,
    hexbin,
    pals,
    MASS,
    sf,
    reticulate,
    LOLA,
    readr,
    SummarizedExperiment,
    DESeq2,
    edgeR,
    purrr,
    ROTS
Suggests:
    knitr,
    formatR,
    rmarkdown,
    testthat (>= 3.0.0),
    highcharter,
    reshape2,
    scales,
    tibble,
    DiffBind,
    gridExtra,
    idr2d,
    lattice,
    lwgeom,
    matrixStats,
    tidyverse,
    ggrepel,
    ggrastr,
    GenomeInfoDb,
    tools,
    forcats,
    gplots,
    stringr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/testthat/start-first: norm_bw,genic_intergenic_scatterplot,pre_clust,generate_clust,annotate_clust,density_based_scatterplot,enrich_clust
Collate:
    'ChIPbinner-package.R'
    'norm_bw.R'
    'pre_clust.R'
    'generate_clust.R'
    'annotate_clust.R'
    'apply_normFactors.R'
    'density_based_scatterplot.R'
    'differentialBinAnalysis.R'
    'enrich_clust.R'
    'filter_low_counts.R'
    'genic_intergenic_scatterplot.R'
    'merge_norm_bw.R'
    'plot_PCA.R'
    'plot_correlation.R'
Depends:
    R (>= 3.5.0)
biocViews:
    ChIPSeq,
    Epigenetics,
    HistoneModification,
    GenomeAnnotation,
    Normalization,
    Clustering,
    PrincipalComponent,
    Visualization,
    Software