1. Gviz
  2. DESCRIPTION
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bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:22:19
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.44.0
3 
+Version: 1.45.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:22:19
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.43.3
3 
+Version: 1.44.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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Fixed colors in histogram and bumped version

Robert Ivánek authored on 25/04/2023 10:06:00
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.43.2
3 
+Version: 1.43.3
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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Bumped version

Robert Ivánek authored on 04/04/2023 13:14:01
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.43.1
3 
+Version: 1.43.2
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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Updated to recent version.

Merge remote-tracking branch 'upstream/master'

# Conflicts:
# DESCRIPTION

Robert Ivánek authored on 17/02/2023 18:36:16
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Fixed documentation. Version bumped.

Robert Ivánek authored on 17/02/2023 18:33:21
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.41.1
3 
+Version: 1.41.2
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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@@ -23,10 +23,10 @@ Description: Genomic data analyses requires integrated visualization
23 23 
     your data.
24 24 
 LazyLoad: yes
25 25 
 Encoding: UTF-8
26 
-RoxygenNote: 7.2.0
26 
+RoxygenNote: 7.2.3.9001
27 27 
 Roxygen: list(markdown = TRUE)
28 28 
 Depends:
29 
-    R (>= 4.2),
29 
+    R (>= 4.3),
30 30 
     methods,
31 31 
     S4Vectors (>= 0.9.25),
32 32 
     IRanges (>= 1.99.18),
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bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:06:41
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 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.42.0
3 
+Version: 1.43.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:06:41
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 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.41.1
3 
+Version: 1.42.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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roxygen update.

Robert Ivánek authored on 21/10/2022 13:56:32
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@@ -23,7 +23,7 @@ Description: Genomic data analyses requires integrated visualization
23 23 
     your data.
24 24 
 LazyLoad: yes
25 25 
 Encoding: UTF-8
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-RoxygenNote: 7.1.2
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+RoxygenNote: 7.2.0
27 27 
 Roxygen: list(markdown = TRUE)
28 28 
 Depends:
29 29 
     R (>= 4.2),
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Bumped version.

Robert Ivánek authored on 03/05/2022 17:45:09
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.41.0
3 
+Version: 1.41.1
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:10:17
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DESCRIPTION
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.40.0
3 
+Version: 1.41.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:10:17
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DESCRIPTION
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.39.6
3 
+Version: 1.40.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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Bumped version.

Robert Ivánek authored on 07/04/2022 13:41:14
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.39.5
3 
+Version: 1.39.6
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"),
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Restructured the code, split according to the class, first version of roxygen2 documentation. Bumped the version.

Robert Ivánek authored on 21/01/2022 15:52:54
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@@ -1,24 +1,30 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.39.4
3 
+Version: 1.39.5
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 
-	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
6 
+	 person("Robert", "Ivanek", role=c("aut", "cre"),
7 
+	        email="robert.ivanek@unibas.ch",
8 
+	        comment=c(ORCID="0000-0002-8403-056X")),
7 9 
 	 person("Arne", "Mueller", role="aut"),
8 10 
 	 person("Steve", "Lianoglou", role="aut"),
9 
-	 person("Ge", "Tan", role="aut", email="ge.tan09@imperial.ac.uk"),
10 
-	 person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu"),
11 
-	 person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"),
11 
+	 person("Ge", "Tan", role="aut"),
12 
+	 person("Lance", "Parsons", role="aut"),
13 
+	 person("Shraddha", "Pai", role="aut"),
12 14 
 	 person("Thomas", "McCarthy", role="ctb"),
13 15 
 	 person("Felix", "Ernst", role="ctb"),
14 16 
 	 person("Mike", "Smith", role="ctb"))
15 
-Description: Genomic data analyses requires integrated visualization
16 
-    of known genomic information and new experimental data.  Gviz uses
17 
+Description: Genomic data analyses requires integrated visualization
18 
+    of known genomic information and new experimental data. Gviz uses
17 19 
     the biomaRt and the rtracklayer packages to perform live
18 20 
     annotation queries to Ensembl and UCSC and translates this to
19 21 
     e.g. gene/transcript structures in viewports of the grid graphics
20 22 
     package. This results in genomic information plotted together with
21 23 
     your data.
24 
+LazyLoad: yes
25 
+Encoding: UTF-8
26 
+RoxygenNote: 7.1.2
27 
+Roxygen: list(markdown = TRUE)
22 28 
 Depends:
23 29 
     R (>= 4.2),
24 30 
     methods,
... ... 
@@ -56,11 +62,37 @@ Suggests:
56 62 
     knitr,
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     rmarkdown,
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     testthat
59 
-Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
60 65 
 biocViews: Visualization, Microarray, Sequencing
61 66 
 URL: https://github.com/ivanek/Gviz
62 67 
 BugReports: https://github.com/ivanek/Gviz/issues
63 68 
 VignetteBuilder: knitr
64 69 
 License: Artistic-2.0
65 
-LazyLoad: yes
66 
-Encoding: UTF-8
70 
+Collate:
71 
+    'utils.R'
72 
+    'ImageMap-class.R'
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+    'DisplayPars-class.R'
74 
+    'GdObject-class.R'
75 
+    'ReferenceTrack-class.R'
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+    'SequenceTrack-class.R'
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+    'RangeTrack-class.R'
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+    'StackedTrack-class.R'
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+    'NumericTrack-class.R'
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+    'DataTrack-class.R'
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+    'AlignmentsTrack-class.R'
82 
+    'AnnotationTrack-class.R'
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+    'GeneRegionTrack-class.R'
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+    'BiomartGeneRegionTrack-class.R'
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+    'CustomTrack-class.R'
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+    'GenomeAxisTrack-class.R'
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+    'Gviz-defunct.R'
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+    'Gviz-deprecated.R'
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+    'HighlightTrack-class.R'
90 
+    'IdeogramTrack-class.R'
91 
+    'OverlayTrack-class.R'
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+    'UcscTrack.R'
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+    'collapsing.R'
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+    'datasets.R'
95 
+    'exportTracks.R'
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+    'grouping.R'
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+    'plotTracks.R'
98 
+    'settings.R'
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Version bump.

Robert Ivánek authored on 10/01/2022 09:19:16
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 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.39.3
3 
+Version: 1.39.4
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Added possibility to use different aggregation functions for running windows (DataTrack)

Robert Ivánek authored on 07/01/2022 17:43:20
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 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.39.2
3 
+Version: 1.39.3
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Code cleanup.

Robert Ivánek authored on 06/01/2022 19:52:50
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@@ -20,7 +20,7 @@ Description: Genomic data analyses requires integrated visualization
20 20 
     package. This results in genomic information plotted together with
21 21 
     your data.
22 22 
 Depends:
23 
-    R (>= 4.0),
23 
+    R (>= 4.2),
24 24 
     methods,
25 25 
     S4Vectors (>= 0.9.25),
26 26 
     IRanges (>= 1.99.18),
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Version bump.

Robert Ivánek authored on 05/01/2022 08:18:12
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.39.1
3 
+Version: 1.39.2
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
Browse code

Pass serialized datasets thru updateObject()

- Pass serialized datasets thru updateObject() in preparation for the
switch to virtual DataFrame.
- The switch to virtual DataFrame will happen soon in the S4Vectors package.

Hervé Pagès authored on 02/11/2021 19:16:34
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.39.0
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+Version: 1.39.1
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:02:00
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.38.0
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+Version: 1.39.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:02:00
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DESCRIPTION
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.37.2
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+Version: 1.38.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Version bump.

Robert Ivánek authored on 02/07/2021 09:39:03
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.37.1
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+Version: 1.37.2
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Bumbed version.

Robert Ivánek authored on 29/05/2021 21:10:13
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.37.0
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+Version: 1.37.1
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Added dependecy on xml2, as suggested in #47

Robert Ivánek authored on 27/05/2021 13:17:48
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DESCRIPTION
History View file @ 9804d94
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@@ -51,6 +51,7 @@ Imports:
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     utils
52 52 
 Suggests:
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     BSgenome.Hsapiens.UCSC.hg19,
54 
+    xml2,
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     BiocStyle,
55 56 
     knitr,
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     rmarkdown,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:51:26
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.36.0
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+Version: 1.37.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:51:26
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.35.6
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+Version: 1.36.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bumped version.

Robert Ivánek authored on 19/04/2021 20:26:06
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.35.5
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+Version: 1.35.6
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Version bump in devel.

Robert Ivánek authored on 14/03/2021 21:57:46
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.35.4
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+Version: 1.35.5
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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added Mike Smith to co-author list

Robert Ivánek authored on 11/01/2021 10:34:32
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DESCRIPTION
History View file @ d15ad47
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@@ -10,7 +10,8 @@ Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu"),
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 	 person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"),
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 	 person("Thomas", "McCarthy", role="ctb"),
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-	 person("Felix", "Ernst", role="ctb"))
13 
+	 person("Felix", "Ernst", role="ctb"),
14 
+	 person("Mike", "Smith", role="ctb"))
14 15 
 Description: Genomic data analyses requires integrated visualization
15 16 
     of known genomic information and new experimental data.  Gviz uses
16 17 
     the biomaRt and the rtracklayer packages to perform live
Browse code

Version bump

Mike Smith authored on 07/01/2021 22:14:30
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@@ -1,6 +1,6 @@
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.35.3
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+Version: 1.35.4
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Bumped version

Robert Ivánek authored on 30/11/2020 09:58:13
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.35.2
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+Version: 1.35.3
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
 	 person("Steffen", "Durinck", role="aut"),
6 6 
 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
Browse code

version bump

Robert Ivánek authored on 23/11/2020 10:29:16
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.35.1
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+Version: 1.35.2
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Bumbed version

Robert Ivánek authored on 17/11/2020 11:05:19
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.35.0
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+Version: 1.35.1
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:44:46
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.34.0
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+Version: 1.35.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:44:46
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.33.2
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+Version: 1.34.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bumped version after fixing bugs introduced by recent changes in BSgenome/GenomeInfoDb packages - providerVersion (non-fucntional) - releaseNmae (not available)

Robert Ivánek authored on 06/07/2020 11:56:22
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.33.1
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+Version: 1.33.2
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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- added test for sashimiTransformation - bumped version

Robert Ivánek authored on 23/06/2020 11:45:00
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.33.0
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+Version: 1.33.1
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:28:31
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.32.0
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+Version: 1.33.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:28:31
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.13
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+Version: 1.32.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Added draft of tests for BiomartTracks, bumbed version, added NEWS.

Robert Ivánek authored on 21/04/2020 12:46:46
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.12
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+Version: 1.31.13
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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added possibility to create GeneRegionTrack from EnsDb

Robert Ivánek authored on 05/03/2020 13:35:36
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@@ -33,6 +33,7 @@ Imports:
33 33 
     AnnotationDbi (>= 1.27.5),
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     Biobase (>= 2.15.3),
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     GenomicFeatures (>= 1.17.22),
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+    ensembldb (>= 2.11.3),
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     BSgenome (>= 1.33.1),
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     Biostrings (>= 2.33.11),
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     biovizBase (>= 1.13.8),
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merged pull request #25, bumped version

Robert Ivánek authored on 04/03/2020 12:54:16
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Fix issue created by .warn_once in DetailedAnnotationTrack. Changes strand methods. Added some more tests.

Robert Ivánek authored on 20/02/2020 11:21:02
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.10
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+Version: 1.31.11
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Clenaup of code (tab to 4spaces)

Robert Ivánek authored on 19/02/2020 20:27:14
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@@ -19,7 +19,7 @@ Description: Genomic data analyses requires integrated visualization
19 19 
     package. This results in genomic information plotted together with
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     your data.
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 Depends:
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-    R (>= 2.10.0),
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+    R (>= 4.0),
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     methods,
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     S4Vectors (>= 0.9.25),
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     IRanges (>= 1.99.18),
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     GenomicAlignments (>= 1.1.16),
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     GenomeInfoDb (>= 1.1.3),
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     BiocGenerics (>= 0.11.3),
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-    digest(>= 0.6.8)
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+    digest(>= 0.6.8),
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+    graphics,
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+    grDevices,
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+    stats,
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+    utils
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 Suggests:
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     BSgenome.Hsapiens.UCSC.hg19,
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     BiocStyle,
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Test for .buildRange change, bumped version

Robert Ivánek authored on 19/02/2020 10:38:07
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1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.9
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+Version: 1.31.10
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Edited readme

Robert Ivánek authored on 17/02/2020 16:46:21
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@@ -2,7 +2,7 @@ Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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 Version: 1.31.9
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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-   person("Steffen", "Durinck", role="aut"),
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+	 person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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 	 person("Arne", "Mueller", role="aut"),
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 	 person("Steve", "Lianoglou", role="aut"),
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@@ -10,7 +10,7 @@ Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	 person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu"),
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 	 person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"),
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 	 person("Thomas", "McCarthy", role="ctb"),
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-	 person(" Felix", "Ernst", role="ctb"))
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+	 person("Felix", "Ernst", role="ctb"))
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 Description: Genomic data analyses requires integrated visualization
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     of known genomic information and new experimental data.  Gviz uses
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     the biomaRt and the rtracklayer packages to perform live
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Bumbed version after adding bunch of tests.

Robert Ivánek authored on 14/02/2020 16:38:05
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.8
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+Version: 1.31.9
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Added possibility to specify circle as an alternative shape for centromere (IdeogramTrack), removed white spaces/lines from documentation.

Robert Ivánek authored on 13/02/2020 12:07:31
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.7
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+Version: 1.31.8
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Added the possibility to visualize the indels in the AlignmentsTrack. Bumped version.

Robert Ivánek authored on 12/02/2020 16:02:35
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.6
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+Version: 1.31.7
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Fixed missing tables in the vignette.

Robert Ivánek authored on 11/02/2020 11:10:21
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.5
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+Version: 1.31.6
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bumbed version

Robert Ivánek authored on 30/01/2020 12:57:40
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.4
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+Version: 1.31.5
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Removed dependency on kableExtra.

Robert Ivánek authored on 28/01/2020 10:11:24
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DESCRIPTION
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@@ -47,7 +47,6 @@ Suggests:
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     BSgenome.Hsapiens.UCSC.hg19,
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     BiocStyle,
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     knitr,
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-    kableExtra,
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     rmarkdown,
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     testthat
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 Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
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Fix problem with coloring the mismatches/reads. Bumped the version.

Robert Ivánek authored on 28/01/2020 08:50:37
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 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.3
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+Version: 1.31.4
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
Browse code

Adapted for errors when setting both Sys.setenv _R_CHECK_LENGTH_1_LOGIC2_ and _R_CHECK_LENGTH_1_CONDITION_ to TRUE

Robert Ivánek authored on 27/01/2020 23:56:22
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.2
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+Version: 1.31.3
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Bumped version to 1.31.2

Robert Ivánek authored on 27/01/2020 11:18:37
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1 1 
 Package: Gviz
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 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.31.1
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+Version: 1.31.2
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
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    person("Steffen", "Durinck", role="aut"),
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 	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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Bumbed version, added Felix Ernst as a co-author

Robert Ivánek authored on 23/01/2020 16:22:05
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@@ -1,15 +1,16 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.31.0
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+Version: 1.31.1
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
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-             person("Steffen", "Durinck", role="aut"),
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-	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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-	     person("Arne", "Mueller", role="aut"),
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-	     person("Steve", "Lianoglou", role="aut"),
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-	     person("Ge", "Tan", role="aut", email="ge.tan09@imperial.ac.uk"),
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-	     person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu"),
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-	     person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"),
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-	     person("Thomas", "McCarthy", role="ctb"))
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+   person("Steffen", "Durinck", role="aut"),
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+	 person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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+	 person("Arne", "Mueller", role="aut"),
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+	 person("Steve", "Lianoglou", role="aut"),
9 
+	 person("Ge", "Tan", role="aut", email="ge.tan09@imperial.ac.uk"),
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+	 person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu"),
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+	 person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"),
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+	 person("Thomas", "McCarthy", role="ctb"),
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+	 person(" Felix", "Ernst", role="ctb"))
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 Description: Genomic data analyses requires integrated visualization
14 15 
     of known genomic information and new experimental data.  Gviz uses
15 16 
     the biomaRt and the rtracklayer packages to perform live
Browse code

Added Thomas McCarthy to description. PR #9

Robert Ivánek authored on 23/01/2020 10:56:26
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DESCRIPTION
History View file @ 289e2cb
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@@ -8,7 +8,8 @@ Authors@R: c(person("Florian", "Hahne", role="aut"),
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 	     person("Steve", "Lianoglou", role="aut"),
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 	     person("Ge", "Tan", role="aut", email="ge.tan09@imperial.ac.uk"),
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 	     person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu"),
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-	     person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"))
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+	     person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"),
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+	     person("Thomas", "McCarthy", role="ctb"))
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 Description: Genomic data analyses requires integrated visualization
13 14 
     of known genomic information and new experimental data.  Gviz uses
14 15 
     the biomaRt and the rtracklayer packages to perform live
Browse code

removed magick and travis part, trying to find minimal settings to get package compiled with travis

Robert Ivánek authored on 22/01/2020 23:29:30
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DESCRIPTION
History View file @ a6ff3a2
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@@ -45,7 +45,6 @@ Suggests:
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     BSgenome.Hsapiens.UCSC.hg19,
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     BiocStyle,
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     knitr,
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-    magick,
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     kableExtra,
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     rmarkdown,
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     testthat
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added magick back to suggested and added corresponding part to travis.yml

Robert Ivánek authored on 22/01/2020 22:39:09
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DESCRIPTION
History View file @ d5f8958
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@@ -45,6 +45,7 @@ Suggests:
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     BSgenome.Hsapiens.UCSC.hg19,
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     BiocStyle,
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     knitr,
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+    magick,
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     kableExtra,
49 50 
     rmarkdown,
50 51 
     testthat
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removed magick from suggested packages

Robert Ivánek authored on 22/01/2020 22:33:43
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DESCRIPTION
History View file @ e88572c
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@@ -45,7 +45,6 @@ Suggests:
45 45 
     BSgenome.Hsapiens.UCSC.hg19,
46 46 
     BiocStyle,
47 47 
     knitr,
48 
-    magick,
49 48 
     kableExtra,
50 49 
     rmarkdown,
51 50 
     testthat
Browse code

added the possibility to specify position of y-axis tick-marks

Robert Ivánek authored on 22/01/2020 22:19:43
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DESCRIPTION
History View file @ 7dde370
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@@ -45,6 +45,7 @@ Suggests:
45 45 
     BSgenome.Hsapiens.UCSC.hg19,
46 46 
     BiocStyle,
47 47 
     knitr,
48 
+    magick,
48 49 
     kableExtra,
49 50 
     rmarkdown,
50 51 
     testthat
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:36:05
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DESCRIPTION
History View file @ 33370fb
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.30.0
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+Version: 1.31.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
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              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:08:27
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DESCRIPTION
History View file @ 1119ca6
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
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-Version: 1.29.3
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+Version: 1.30.0
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 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
Browse code

Fixed bug created when naming the colors, pch, cex... in case of grouping Bumped version

Robert Ivánek authored on 16/09/2019 16:15:40
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DESCRIPTION
History View file @ 0006b38
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.29.2
3 
+Version: 1.29.3
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
Browse code

Bumped version.

Robert Ivánek authored on 16/09/2019 15:02:01
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.29.1
3 
+Version: 1.29.2
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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version bump 1.29.1, to propagate the changes in devel

Robert Ivánek authored on 15/08/2019 09:56:47
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.29.0
3 
+Version: 1.29.1
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:11:10
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.28.0
3 
+Version: 1.29.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:34
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DESCRIPTION
History View file @ 79262cc
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.27.8
3 
+Version: 1.28.0
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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bumbed version for 3.9 to iclude last commits

Robert Ivánek authored on 29/04/2019 09:46:33
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DESCRIPTION
History View file @ 8fde3f0
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@@ -1,6 +1,6 @@
1 1 
 Package: Gviz
2 2 
 Title: Plotting data and annotation information along genomic coordinates
3 
-Version: 1.27.7
3 
+Version: 1.27.8
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
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removed additional typo in package description

Robert Ivánek authored on 29/04/2019 09:27:44
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DESCRIPTION
History View file @ 4619fbf
... ... 
@@ -7,7 +7,7 @@ Authors@R: c(person("Florian", "Hahne", role="aut"),
7 7 
 	     person("Arne", "Mueller", role="aut"),
8 8 
 	     person("Steve", "Lianoglou", role="aut"),
9 9 
 	     person("Ge", "Tan", role="aut", email="ge.tan09@imperial.ac.uk"),
10 
-	     person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu")
10 
+	     person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu"),
11 11 
 	     person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"))
12 12 
 Description: Genomic data analyses requires integrated visualization
13 13 
     of known genomic information and new experimental data.  Gviz uses
Browse code

removed typos in package description

Robert Ivánek authored on 29/04/2019 09:23:16
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DESCRIPTION
History View file @ 2557ec6
... ... 
@@ -4,11 +4,11 @@ Version: 1.27.7
4 4 
 Authors@R: c(person("Florian", "Hahne", role="aut"),
5 5 
              person("Steffen", "Durinck", role="aut"),
6 6 
 	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
7 
-	     person("Arne","Mueller", role="aut"),
7 
+	     person("Arne", "Mueller", role="aut"),
8 8 
 	     person("Steve", "Lianoglou", role="aut"),
9 
-	     person("Ge","Tan", email="ge.tan09@imperial.ac.uk", role="aut"),
10 
-	     person("Lance","Parsons", email="lparsons@princeton.edu", role="aut"),
11 
-	     person("Shraddha Pai", email="shraddha.pai@utoronto.ca", role="aut"))
9 
+	     person("Ge", "Tan", role="aut", email="ge.tan09@imperial.ac.uk"),
10 
+	     person("Lance", "Parsons", role="aut", email="lparsons@princeton.edu")
11 
+	     person("Shraddha", "Pai", role="aut", email="shraddha.pai@utoronto.ca"))
12 12 
 Description: Genomic data analyses requires integrated visualization
13 13 
     of known genomic information and new experimental data.  Gviz uses
14 14 
     the biomaRt and the rtracklayer packages to perform live
Browse code

added news, reformatted package description

Robert Ivánek authored on 29/04/2019 09:21:09
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DESCRIPTION
History View file @ 4777291
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@@ -1,14 +1,58 @@
1 1 
 Package: Gviz
2 
-Version: 1.27.7
3 2 
 Title: Plotting data and annotation information along genomic coordinates
4 
-Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
5 
-Maintainer: Robert Ivanek <robert.ivanek@unibas.ch>
6 
-Depends: R (>= 2.10.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid
7 
-Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8)
8 
-Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, kableExtra, rmarkdown, testthat
9 
-VignetteBuilder: knitr
10 
-biocViews: Visualization, Microarray
11 
-Description: Genomic data analyses requires integrated visualization of known genomic information and new experimental data.  Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
3 
+Version: 1.27.7
4 
+Authors@R: c(person("Florian", "Hahne", role="aut"),
5 
+             person("Steffen", "Durinck", role="aut"),
6 
+	     person("Robert", "Ivanek", role=c("aut", "cre"), email="robert.ivanek@unibas.ch", comment=c(ORCID="0000-0002-8403-056X")),
7 
+	     person("Arne","Mueller", role="aut"),
8 
+	     person("Steve", "Lianoglou", role="aut"),
9 
+	     person("Ge","Tan", email="ge.tan09@imperial.ac.uk", role="aut"),
10 
+	     person("Lance","Parsons", email="lparsons@princeton.edu", role="aut"),
11 
+	     person("Shraddha Pai", email="shraddha.pai@utoronto.ca", role="aut"))
12 
+Description: Genomic data analyses requires integrated visualization
13 
+    of known genomic information and new experimental data.  Gviz uses
14 
+    the biomaRt and the rtracklayer packages to perform live
15 
+    annotation queries to Ensembl and UCSC and translates this to
16 
+    e.g. gene/transcript structures in viewports of the grid graphics
17 
+    package. This results in genomic information plotted together with
18 
+    your data.
19 
+Depends:
20 
+    R (>= 2.10.0),
21 
+    methods,
22 
+    S4Vectors (>= 0.9.25),
23 
+    IRanges (>= 1.99.18),
24 
+    GenomicRanges (>= 1.17.20),
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+    grid
26 
+Imports:
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+    XVector (>= 0.5.7),
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+    rtracklayer (>= 1.25.13),
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+    lattice, RColorBrewer,
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+    biomaRt (>= 2.11.0),
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+    AnnotationDbi (>= 1.27.5),
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+    Biobase (>= 2.15.3),
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+    GenomicFeatures (>= 1.17.22),
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+    BSgenome (>= 1.33.1),
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+    Biostrings (>= 2.33.11),
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+    biovizBase (>= 1.13.8),
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+    Rsamtools (>= 1.17.28),
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+    latticeExtra (>= 0.6-26),
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+    matrixStats (>= 0.8.14),
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+    GenomicAlignments (>= 1.1.16),
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+    GenomeInfoDb (>= 1.1.3),
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+    BiocGenerics (>= 0.11.3),
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+    digest(>= 0.6.8)
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+Suggests:
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+    BSgenome.Hsapiens.UCSC.hg19,
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+    BiocStyle,
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+    knitr,
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+    kableExtra,
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+    rmarkdown,
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+    testthat
12 51 
 Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
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+biocViews: Visualization, Microarray, Sequencing
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+URL: https://github.com/ivanek/Gviz
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+BugReports: https://github.com/ivanek/Gviz/issues
55 
+VignetteBuilder: knitr
13 56 
 License: Artistic-2.0
14 57 
 LazyLoad: yes
58 
+Encoding: UTF-8
Browse code

fixed issues with hg19 and biomaRt

Robert Ivánek authored on 23/04/2019 20:48:25
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DESCRIPTION
History View file @ 83788ac
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@@ -1,5 +1,5 @@
1 1 
 Package: Gviz
2 
-Version: 1.27.6
2 
+Version: 1.27.7
3 3 
 Title: Plotting data and annotation information along genomic coordinates
4 4 
 Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
5 5 
 Maintainer: Robert Ivanek <robert.ivanek@unibas.ch>
Browse code

bumped version to 1.27.6

Robert Ivánek authored on 21/02/2019 10:20:39
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DESCRIPTION
History View file @ 6275a0b
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@@ -1,5 +1,5 @@
1 1 
 Package: Gviz
2 
-Version: 1.27.5
2 
+Version: 1.27.6
3 3 
 Title: Plotting data and annotation information along genomic coordinates
4 4 
 Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
5 5 
 Maintainer: Robert Ivanek <robert.ivanek@unibas.ch>
Browse code

bumped package version to 1.27.5

Robert Ivánek authored on 03/01/2019 13:00:29
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DESCRIPTION
History View file @ c9773d2
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@@ -1,5 +1,5 @@
1 1 
 Package: Gviz
2 
-Version: 1.27.4
2 
+Version: 1.27.5
3 3 
 Title: Plotting data and annotation information along genomic coordinates
4 4 
 Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
5 5 
 Maintainer: Robert Ivanek <robert.ivanek@unibas.ch>
Browse code

version bump, new HTML vignette

Robert Ivánek authored on 11/12/2018 12:34:49
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DESCRIPTION
History View file @ 7e787ad
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@@ -1,5 +1,5 @@
1 1 
 Package: Gviz
2 
-Version: 1.27.3
2 
+Version: 1.27.4
3 3 
 Title: Plotting data and annotation information along genomic coordinates
4 4 
 Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
5 5 
 Maintainer: Robert Ivanek <robert.ivanek@unibas.ch>
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changed vignette to html (knitr based)

Robert Ivánek authored on 10/12/2018 23:48:08
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DESCRIPTION
History View file @ 8804b2c
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@@ -5,7 +5,8 @@ Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Liano
5 5 
 Maintainer: Robert Ivanek <robert.ivanek@unibas.ch>
6 6 
 Depends: R (>= 2.10.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid
7 7 
 Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8)
8 
-Suggests: xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, testthat
8 
+Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, kableExtra, rmarkdown, testthat
9 
+VignetteBuilder: knitr
9 10 
 biocViews: Visualization, Microarray
10 11 
 Description: Genomic data analyses requires integrated visualization of known genomic information and new experimental data.  Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
11 12 
 Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
Browse code

added testthat support

Robert Ivánek authored on 10/12/2018 13:35:21
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DESCRIPTION
History View file @ ce80637
... ... 
@@ -3,12 +3,11 @@ Version: 1.27.3
3 3 
 Title: Plotting data and annotation information along genomic coordinates
4 4 
 Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
5 5 
 Maintainer: Robert Ivanek <robert.ivanek@unibas.ch>
6 
-Depends:  R (>= 2.10.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid
6 
+Depends: R (>= 2.10.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid
7 7 
 Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8)
8 
-Suggests: xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle
8 
+Suggests: xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, testthat
9 9 
 biocViews: Visualization, Microarray
10 10 
 Description: Genomic data analyses requires integrated visualization of known genomic information and new experimental data.  Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
11 11 
 Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
12 12 
 License: Artistic-2.0
13 13 
 LazyLoad: yes
14