-
Notifications
You must be signed in to change notification settings - Fork 13
/
Copy pathNEWS
executable file
·194 lines (105 loc) · 4.49 KB
/
NEWS
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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
CHANGES in VERSION 2.5.2
- add `getGeneSetsFromOrgDb()`
------------------------------------------
CHANGES in VERSION 2.5.1
- support extending from the whole genes
------------------------------------------
CHANGES in VERSION 2.1.9
- add `getKEGGGenome()`
------------------------------------------
CHANGES in VERSION 2.1.8
- add `getGenomeDateFromNCBI()`
-------------------------------------------
CHANGES in VERSION 2.1.4
* online great: the names of input regions are kept.
* region coordinates (1-based or zero-based) are adjusted in `getRegionGeneAssociations()`.
-------------------------------------------
CHANGES in VERSION 1.99.7
* Calculation has been speeded up.
--------------------------------------------
CHANGES in VERSION 1.99.6
* set `getGeneSetsFromBioMart()` public
---------------------------------------------
CHANGES in VERSION 1.99.2
* by default exclude gap regions
* chr prefix in `gr` is removed when `biomart_dataset` is set.
-----------------------------------------------
CHANGES in VERSION 1.99.0
* add `great()` and related functions to support local GREAT.
* add `shinyReport()` to export results into a shiny application.
-----------------------------------------------
CHANGES in VERSION 1.21.1
* parseRegionGeneAssociationFile(): parsing also considers positions with no sign.
-----------------------------------------------
CHANGES in VERSION 1.19.1
* add 'tsv' option in `getEnrichmentTables()`
------------------------------------------------
CHANGES in VERSION 1.17.1
* assign to foreName and backName when querying GREAT
* use rmarkdown for vignette
* support GREAT version 4.0.4
* add startup messages
------------------------------------------------
CHANGES in VERSION 1.15.1
* `plotRegionGeneAssociationGraphs()`: fixe a bug of wrong value of `par(mfrow)`.
* fixed warnings of Rd files.
-------------------------------------------------
CHANGES in VERSION 1.13.3
* parse error message from GREAT
---------------------------------------------------
CHANGES in VERSION 1.13.1
* `plotRegionGeneAssociationGraphs()`: `par(mfrow)` is automatically set
according to the length of `type`.
----------------------------------------------------
CHANGES in VERSION 1.11.1
* save regions in gzip file then submit to GREAT
* will not change the content of the input regions
----------------------------------------------------
CHANGES in VERSION 1.9.1
* change url according to changes on GREAT website
-----------------------------------------------------
CHANGES in VERSION 1.7.1
* submitGreatJob(): remove additional column by pintersect()
-----------------------------------------------------
CHANGES in VERSION 1.5.3
* if background is provided, input regions are automaticially adjusted
to make sure all input regions are subset of backgrounds.
------------------------------------------------------
CHANGES in VERSION 1.3.3
* documentations were improved.
* test files are moved to tests/testthat
--------------------------------------------------------
CHANGES in VERSION 1.3.2
* bug fixed when background is self-provided.
--------------------------------------------------------
CHANGES in VERSION 1.3.1
* fixed a bug when gene symbol annotated by GREAT is ''
* print warnings when GREAT gives warnings
--------------------------------------------------------
CHANGES in VERSION 1.1.6
* versions of GREAT can be selected
--------------------------------------------------------
CHANGES in VERSION 1.1.5
* minor changes in documentations
---------------------------------------------------------
CHANGES in VERSION 1.1.4
* minor changes to adjust to github mirror
----------------------------------------------------------
CHANGES in VERSION 1.1.3
* error message is extract from GREAT now.
* default value of `bgChoice` depeneds on `gr`
-----------------------------------------------------------
CHANGES in VERSION 1.1.2
* add dependency to base packages
-----------------------------------------------------------
CHANGES in VERSION 1.1.1
* enrivonment for the slots in `GreatJob` object are initialized
inside `submitGreatJob`
-----------------------------------------------------------
CHANGES IN VERSION 0.99.5
* because analysis depends on internet connection, jump to
next version to enforce rebuilding of the vignette on bioconductor.
------------------------------------------------------------
CHANGES IN VERSION 0.99.4
* retrieve categories and corresponding ontologies from GREAT
------------------------------------------------------------