|
1 |
| -Package: ggcoverage |
2 | 1 | Type: Package
|
| 2 | +Package: ggcoverage |
3 | 3 | Title: Visualize Genome/Protein Coverage with Various Annotations
|
4 | 4 | Version: 1.3.0
|
5 | 5 | Authors@R: c(
|
6 |
| - person(given = "Yabing", |
7 |
| - family = "Song", |
8 |
| - role = c("aut", "cre"), |
9 |
| - |
10 |
| - person(given = "Michael", |
11 |
| - family = "Jahn", |
12 |
| - |
13 |
| - role = "aut", |
| 6 | + person("Yabing", "Song", , " [email protected]", role = c("aut", "cre", "cph")), |
| 7 | + person("Michael", "Jahn", , " [email protected]", role = c("aut", "cph"), |
14 | 8 | comment = c(ORCID = "0000-0002-3913-153X"))
|
15 | 9 | )
|
16 | 10 | Maintainer: Yabing Song < [email protected]>
|
17 |
| -Description: The goal of 'ggcoverage' is to simplify the process of visualizing genome/protein coverage. It contains functions to |
18 |
| - load data from BAM, BigWig, BedGraph or txt/xlsx files, create genome/protein coverage plot, add various annotations to |
19 |
| - the coverage plot, including base and amino acid annotation, GC annotation, gene annotation, transcript annotation, ideogram annotation, |
20 |
| - peak annotation, contact map annotation, link annotation and peotein feature annotation. |
| 11 | +Description: The goal of 'ggcoverage' is to simplify the process of |
| 12 | + visualizing genome/protein coverage. It contains functions to load |
| 13 | + data from BAM, BigWig, BedGraph or txt/xlsx files, create |
| 14 | + genome/protein coverage plots, add various annotations to the coverage |
| 15 | + plot, including base and amino acid annotation, GC annotation, gene |
| 16 | + annotation, transcript annotation, ideogram annotation, peak |
| 17 | + annotation, contact map annotation, link annotation and protein |
| 18 | + feature annotation. |
21 | 19 | License: MIT + file LICENSE
|
22 |
| -Encoding: UTF-8 |
23 |
| -RoxygenNote: 7.3.1 |
24 |
| -URL: https://showteeth.github.io/ggcoverage/, https://github.com/showteeth/ggcoverage |
| 20 | +URL: https://showteeth.github.io/ggcoverage/, |
| 21 | + https://github.com/showteeth/ggcoverage |
25 | 22 | BugReports: https://github.com/showteeth/ggcoverage/issues
|
26 |
| -biocViews: |
27 | 23 | Imports:
|
| 24 | + BiocParallel, |
| 25 | + Biostrings, |
| 26 | + BSgenome, |
28 | 27 | dplyr,
|
| 28 | + GenomeInfoDb, |
| 29 | + GenomicAlignments, |
29 | 30 | GenomicRanges,
|
30 | 31 | ggbio,
|
| 32 | + ggforce, |
31 | 33 | ggh4x,
|
| 34 | + ggpattern, |
32 | 35 | ggplot2,
|
33 | 36 | ggrepel,
|
34 | 37 | grDevices,
|
| 38 | + gridExtra, |
| 39 | + HiCBricks, |
35 | 40 | IRanges,
|
36 | 41 | magrittr,
|
| 42 | + methods, |
| 43 | + openxlsx, |
37 | 44 | patchwork,
|
38 | 45 | RColorBrewer,
|
| 46 | + reshape2, |
39 | 47 | rlang,
|
40 | 48 | Rsamtools,
|
41 | 49 | rtracklayer,
|
42 |
| - scales, |
43 |
| - stats, |
44 |
| - utils, |
45 |
| - methods, |
46 |
| - GenomeInfoDb, |
47 | 50 | S4Vectors,
|
48 |
| - Biostrings, |
49 |
| - BSgenome, |
50 |
| - GenomicAlignments, |
51 |
| - reshape2, |
| 51 | + scales, |
52 | 52 | seqinr,
|
53 |
| - ggforce, |
54 |
| - HiCBricks, |
55 |
| - ggpattern, |
56 |
| - BiocParallel, |
57 |
| - openxlsx, |
| 53 | + stats, |
58 | 54 | stringr,
|
59 |
| - gridExtra |
| 55 | + utils |
60 | 56 | Suggests:
|
61 |
| - rmarkdown, |
62 |
| - knitr, |
63 | 57 | BiocStyle,
|
64 |
| - htmltools, |
65 | 58 | BSgenome.Hsapiens.UCSC.hg19,
|
66 | 59 | graphics,
|
67 |
| - HiCDataHumanIMR90 |
68 |
| -VignetteBuilder: knitr |
| 60 | + HiCDataHumanIMR90, |
| 61 | + htmltools, |
| 62 | + knitr, |
| 63 | + rmarkdown |
| 64 | +VignetteBuilder: |
| 65 | + knitr |
| 66 | +biocViews: |
| 67 | +Encoding: UTF-8 |
| 68 | +RoxygenNote: 7.3.1 |
0 commit comments