PATO/DESCRIPTION at master · irycisBioinfo/PATO · 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: pato
Type: Package
Title: Pangenome Analysis Toolkit
Version: 1.0.6
Author: Miguel Diez Fernandez de Bobadilla
	Alba Talavera Rodríguez
	Lucia Chacon Vargas
	Fernando Baquero
	Teresa M. Coque
	Val F. Lanza <valfernandez.vf@gmail.com>
Maintainer: Val F. Lanza <valfernandez.vf@gmail.com>
Description: PATO is a R package designed to analyze pangenomes (set of genomes)
	intra or inter species. It allows to analyze the core-genome, accessory
	genome and whole genome, the population structure, and the horizontal
	gene transfer dynamics. PATO uses, as core software MASH, MMSeq2, Minimap2 and R.
License: CC0
Encoding: UTF-8
LazyData: true
Imports:
 ggplot2 (>= 3.1.1),
 tibble (>= 2.1.3),
 htmlwidgets (>= 1.3),
 htmltools (>= 0.4.0),
 threejs (>= 0.3.1),
 igraph (>= 1.2.4.1),
 uwot (>= 0.1.3),
 tidyr (>= 0.8.3),
 dplyr (>= 1.0.0),
 dtplyr (>= 0.0.3),
 data.table (>= 1.12.2),
 phangorn (>= 2.5.5),
 randomcoloR (>= 1.1.0),
 magrittr (>= 1.5),
 Rcpp (>= 1.0.2),
 mclust (>= 5.4.5),
 dbscan (>= 1.1-4),
 ape (>= 5.3),
 parallelDist (>= 0.2.4),
 foreach (>= 1.5.0),
 doParallel (>= 1.0.15),
 parallel (>= 3.5.2),
 manipulateWidget (>= 0.10.0),
 stringr (>= 1.4.0),
 stringdist (>= 0.9.6),
 openssl (>= 1.4.3),
 Biostrings (>= 2.52.0),
 microseq (>= 2.1.2)
Suggests:
    pheatmap (>= 1.0.12),
    knitr,
    rmarkdown
BinaryFiles:
 mash
 mash.macos
 mmseqs.avx2
 mmseqs.sse41
 mmseqs.macos.avx2
 mmseqs.macos.sse41
 minimap2
 bedtools
 k8
Roxygen:
    list(markdown = TRUE)
RoxygenNote: 7.2.0
VignetteBuilder: knitr