-
Notifications
You must be signed in to change notification settings - Fork 0
/
DESCRIPTION
86 lines (86 loc) · 2.63 KB
/
DESCRIPTION
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
Package: universalmotif
Title: Import, Modify, and Export Motifs with R
Version: 1.23.1
Authors@R: c(
person(c("Benjamin", "Jean-Marie"), "Tremblay", role = c("aut", "cre"),
email = "benjamin.tremblay@uwaterloo.ca",
comment = c(ORCID = "0000-0002-7441-2951")),
person("Spencer", "Nystrom", role = "ctb",
comment = c(ORCID = "0000-0003-1000-1579"))
)
URL: https://bioconductor.org/packages/universalmotif/
BugReports: https://github.com/bjmt/universalmotif/issues
Description: Allows for importing most common motif types into R for use by
functions provided by other Bioconductor motif-related packages. Motifs can
be exported into most major motif formats from various classes as defined
by other Bioconductor packages. A suite of motif and sequence manipulation
and analysis functions are included, including enrichment, comparison,
P-value calculation, shuffling, trimming, higher-order motifs, and others.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp,
Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics
Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat,
BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx,
ggseqlogo, cowplot, GenomicRanges, ggbio
Enhances: PWMEnrich, rGADEM
LinkingTo: Rcpp, RcppThread
VignetteBuilder: knitr
biocViews: MotifAnnotation, MotifDiscovery, DataImport, GeneRegulation
RoxygenNote: 7.1.2
Roxygen: list(markdown = TRUE, old_usage = TRUE)
Language: en-GB
Collate:
'RcppExports.R'
'add_multifreq.R'
'compare_motifs.R'
'universalmotif-class.R'
'convert_motifs.R'
'convert_type.R'
'create_motif.R'
'create_sequences.R'
'data.R'
'enrich_motifs.R'
'filter_motifs.R'
'get_bkg.R'
'make_DBscores.R'
'merge_motifs.R'
'merge_similar.R'
'motif_clusters.R'
'motif_finder.R'
'motif_peaks.R'
'motif_pvalue.R'
'motif_rc.R'
'motif_tree.R'
'read_cisbp.R'
'read_homer.R'
'read_jaspar.R'
'read_matrix.R'
'read_meme.R'
'read_motifs.R'
'read_transfac.R'
'read_uniprobe.R'
'run_meme.R'
'sample_sites.R'
'scan_sequences.R'
'sequence_complexity.R'
'shuffle_motifs.R'
'shuffle_sequences.R'
'switch_alph.R'
'trim_motifs.R'
'universalmotif-methods.R'
'universalmotif.R'
'universalmotif_df.R'
'utils-internal.R'
'utils-motif.R'
'utils-sequence.R'
'view_logo.R'
'view_motifs.R'
'write_homer.R'
'write_jaspar.R'
'write_matrix.R'
'write_meme.R'
'write_motifs.R'
'write_transfac.R'
'zzz.R'