1. MotifDb
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:07:15
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DESCRIPTION
History View file @ 113732b
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.40.0
4 
+Version: 1.41.0
5 5 
 Date: 2022-03-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:07:15
Showing 1 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.39.0
4 
+Version: 1.40.0
5 5 
 Date: 2022-03-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:11:46
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DESCRIPTION
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1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.38.0
4 
+Version: 1.39.0
5 5 
 Date: 2022-03-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:11:45
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DESCRIPTION
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1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.37.2
4 
+Version: 1.38.0
5 5 
 Date: 2022-03-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

updated show method, renamed to makefile

paul-shannon authored on 04/03/2022 21:16:37
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DESCRIPTION
History View file @ 5b92878
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.37.1
4 
+Version: 1.37.2
5 5 
 Date: 2022-03-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

legal version bump

paul-shannon authored on 04/03/2022 20:49:59
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DESCRIPTION
History View file @ 01b1ed7
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.38.0
4 
+Version: 1.37.1
5 5 
 Date: 2022-03-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

jaspar2022 added

paul-shannon authored on 04/03/2022 20:48:22
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DESCRIPTION
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.37.0
5 
-Date: 2021-10-03
4 
+Version: 1.38.0
5 
+Date: 2022-03-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:04:11
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.36.0
4 
+Version: 1.37.0
5 5 
 Date: 2021-10-03
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:04:11
Showing 1 changed files
DESCRIPTION
History View file @ 7e45029
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.35.6
4 
+Version: 1.36.0
5 5 
 Date: 2021-10-03
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

fixed onload error, moved tfs RData file to tfs directory

paul-shannon authored on 03/10/2021 15:37:53
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DESCRIPTION
History View file @ 8feeb4a
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.35.5
5 
-Date: 2021-09-01
4 
+Version: 1.35.6
5 
+Date: 2021-10-03
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Browse code

suggests markdown

paul-shannon authored on 01/09/2021 17:30:30
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DESCRIPTION
History View file @ 3fc5bd6
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@@ -1,12 +1,12 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.35.4
5 
-Date: 2021-08-25
4 
+Version: 1.35.5
5 
+Date: 2021-09-01
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
9 
-Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR
9 
+Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
... ... 
@@ -17,5 +17,6 @@ biocViews: MotifAnnotation
17 17 
 VignetteBuilder:
18 18 
   knitr,
19 19 
   rmarkdown,
20 
-  formatR
20 
+  formatR,
21 
+  markdown
21 22 
 Encoding: UTF-8
Browse code

bumped version number

paul-shannon authored on 25/08/2021 18:01:30
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DESCRIPTION
History View file @ fd88b87
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.35.3
4 
+Version: 1.35.4
5 5 
 Date: 2021-08-25
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

removed all mention of markdown package

paul-shannon authored on 25/08/2021 17:49:02
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DESCRIPTION
History View file @ 5b27be4
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@@ -1,12 +1,12 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.35.2
5 
-Date: 2021-08-23
4 
+Version: 1.35.3
5 
+Date: 2021-08-25
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 
-Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, markdown
9 
-Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown
8 
+Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
9 
+Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
Browse code

fixed knitr error

paul-shannon authored on 23/08/2021 15:17:04
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DESCRIPTION
History View file @ d5cce9f
... ... 
@@ -1,11 +1,11 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.35.0
5 
-Date: 2020-04-21
4 
+Version: 1.35.2
5 
+Date: 2021-08-23
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 
-Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
8 
+Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, markdown
9 9 
 Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
... ... 
@@ -15,5 +15,7 @@ License_restricts_use: yes
15 15 
 LazyLoad: yes
16 16 
 biocViews: MotifAnnotation
17 17 
 VignetteBuilder:
18 
-  knitr
18 
+  knitr,
19 
+  rmarkdown,
20 
+  formatR
19 21 
 Encoding: UTF-8
Browse code

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

Nitesh Turaga authored on 19/05/2021 15:53:25
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DESCRIPTION
History View file @ 97ed561
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.34.0
4 
+Version: 1.35.0
5 5 
 Date: 2020-04-21
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:53:25
Showing 1 changed files
DESCRIPTION
History View file @ ed81ab9
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.33.0
4 
+Version: 1.34.0
5 5 
 Date: 2020-04-21
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:46:46
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DESCRIPTION
History View file @ 0e13afe
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.32.0
4 
+Version: 1.33.0
5 5 
 Date: 2020-04-21
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:46:46
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DESCRIPTION
History View file @ 99f1d5a
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.31.0
4 
+Version: 1.32.0
5 5 
 Date: 2020-04-21
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:30:46
Showing 1 changed files
DESCRIPTION
History View file @ 1aef8fe
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.30.0
4 
+Version: 1.31.0
5 5 
 Date: 2020-04-21
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:30:46
Showing 1 changed files
DESCRIPTION
History View file @ 760cd7e
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.12
4 
+Version: 1.30.0
5 5 
 Date: 2020-04-21
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

knitr now SUGGESTED

paul-shannon authored on 21/04/2020 14:40:19
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DESCRIPTION
History View file @ 1a97e0d
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@@ -1,12 +1,12 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.11
5 
-Date: 2020-04-14
4 
+Version: 1.29.12
5 
+Date: 2020-04-21
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
9 
-Suggests: RUnit, seqLogo
9 
+Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
Browse code

bumped version to catch new knitr vignette, updated NEWS

paul-shannon authored on 14/04/2020 16:58:57
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DESCRIPTION
History View file @ 1a90fb1
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.9
5 
-Date: 2020-04-04
4 
+Version: 1.29.11
5 
+Date: 2020-04-14
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
... ... 
@@ -14,3 +14,6 @@ License_is_FOSS: no
14 14 
 License_restricts_use: yes
15 15 
 LazyLoad: yes
16 16 
 biocViews: MotifAnnotation
17 
+VignetteBuilder:
18 
+  knitr
19 
+Encoding: UTF-8
Browse code

removed MotIV from suggests

paul-shannon authored on 04/04/2020 18:02:19
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DESCRIPTION
History View file @ 8cc16fa
... ... 
@@ -6,7 +6,7 @@ Date: 2020-04-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
9 
-Suggests: RUnit, seqLogo, MotIV
9 
+Suggests: RUnit, seqLogo
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
Browse code

removed MotIV from unitTests

paul-shannon authored on 04/04/2020 17:59:55
Showing 1 changed files
DESCRIPTION
History View file @ 28a9214
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.8
5 
-Date: 2020-04-02
4 
+Version: 1.29.9
5 
+Date: 2020-04-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Browse code

removed motifmatchr and its dependencies

paul-shannon authored on 02/04/2020 20:20:03
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DESCRIPTION
History View file @ a3aca6d
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@@ -1,13 +1,13 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.6
5 
-Date: 2020-03-18
4 
+Version: 1.29.8
5 
+Date: 2020-04-02
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
9 
-Suggests: RUnit
10 
-Imports: rtracklayer, splitstackshape, TFBSTools, universalmotif, motifmatchr
9 
+Suggests: RUnit, seqLogo, MotIV
10 
+Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
13 13 
 License_is_FOSS: no
Browse code

hocomoco core|secondary names now used for matrices & rownames mcols

paul-shannon authored on 18/03/2020 20:22:29
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DESCRIPTION
History View file @ 2d7af58
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.4
4 
+Version: 1.29.6
5 5 
 Date: 2020-03-18
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

non-core hocomocov11 motifs tagged 'full' now 'secondary'

paul-shannon authored on 18/03/2020 19:22:54
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DESCRIPTION
History View file @ fe1bab0
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.3
5 
-Date: 2020-03-16
4 
+Version: 1.29.4
5 
+Date: 2020-03-18
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Browse code

hocomoco v11 can be queried by core|full and reliability (A-D)

paul-shannon authored on 16/03/2020 23:36:31
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DESCRIPTION
History View file @ f56272b
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.2
5 
-Date: 2020-03-09
4 
+Version: 1.29.3
5 
+Date: 2020-03-16
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Browse code

fixed version number

paul-shannon authored on 10/03/2020 00:09:45
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DESCRIPTION
History View file @ 62c3f77
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.30.1
4 
+Version: 1.29.2
5 5 
 Date: 2020-03-09
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

provisional addition of hocomoco v1, with reliability scores, A-D

paul-shannon authored on 10/03/2020 00:06:57
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DESCRIPTION
History View file @ 5b88116
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@@ -1,13 +1,13 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.29.0
5 
-Date: 2018-10-24
4 
+Version: 1.30.1
5 
+Date: 2020-03-09
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 
-Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
8 
+Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
9 9 
 Suggests: RUnit
10 
-Imports: rtracklayer, splitstackshape
10 
+Imports: rtracklayer, splitstackshape, TFBSTools, universalmotif, motifmatchr
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
13 13 
 License_is_FOSS: no
Browse code

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

Nitesh Turaga authored on 29/10/2019 17:36:20
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DESCRIPTION
History View file @ 04ce14e
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.28.0
4 
+Version: 1.29.0
5 5 
 Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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 17:08:33
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DESCRIPTION
History View file @ 3602d2b
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.27.0
4 
+Version: 1.28.0
5 5 
 Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

merge

paul-shannon authored on 06/05/2019 18:53:08
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Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:11:14
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DESCRIPTION
History View file @ 5c623f6
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.26.0
4 
+Version: 1.27.0
5 5 
 Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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 15:53:37
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.25.0
4 
+Version: 1.26.0
5 5 
 Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

depends now on R 3.5.0, not 3.5.1

paul-shannon authored on 03/11/2018 19:21:49
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@@ -5,7 +5,7 @@ Version: 1.23.14
5 5 
 Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 
-Depends: R (>= 3.5.1), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
8 
+Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
9 9 
 Suggests: RUnit
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:30
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DESCRIPTION
History View file @ f118237
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1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.24.0
4 
+Version: 1.25.0
5 5 
 Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:49
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.23.14
4 
+Version: 1.24.0
5 5 
 Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

improved docs for query method

paul-shannon authored on 24/10/2018 19:02:56
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DESCRIPTION
History View file @ 5da060a
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@@ -1,11 +1,11 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.23.13
5 
-Date: 2018-10-18
4 
+Version: 1.23.14
5 
+Date: 2018-10-24
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 
-Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
8 
+Depends: R (>= 3.5.1), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
9 9 
 Suggests: RUnit
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
Browse code

big speedup of associateTranscriptionFactors method, exploiting duplicate motifs

paul-shannon authored on 18/10/2018 14:18:37
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DESCRIPTION
History View file @ 4b66948
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.23.11
5 
-Date: 2018-06-17
4 
+Version: 1.23.13
5 
+Date: 2018-10-18
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

added explicit return from plotMotifs

paul-shannon authored on 17/08/2018 16:54:08
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DESCRIPTION
History View file @ 42f0181
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@@ -1,12 +1,12 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.23.9
5 
-Date: 2018-05-23
4 
+Version: 1.23.11
5 
+Date: 2018-06-17
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 
-Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings, motifStack
9 
-Suggests: RUnit, seqLogo, MotIV
8 
+Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
9 
+Suggests: RUnit
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
Browse code

motif/tf mapping now includes the 'both' option, tfclass and motifdb. motifStack plotting added

paul-shannon authored on 03/06/2018 18:31:01
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DESCRIPTION
History View file @ 48c3af4
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@@ -1,11 +1,11 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.23.8
4 
+Version: 1.23.9
5 5 
 Date: 2018-05-23
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 
-Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
8 
+Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings, motifStack
9 9 
 Suggests: RUnit, seqLogo, MotIV
10 10 
 Imports: rtracklayer, splitstackshape
11 11 
 Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
Browse code

motifToGene fix: now combined empty source table with populated table

paul-shannon authored on 23/05/2018 18:32:17
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DESCRIPTION
History View file @ 9535d30
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.21.7
5 
-Date: 2018-05-18
4 
+Version: 1.23.8
5 
+Date: 2018-05-23
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

associateTranscriptionFactors greatly simplified, builds upon motifToGene

paul-shannon authored on 18/05/2018 23:22:10
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DESCRIPTION
History View file @ fda2dea
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@@ -1,14 +1,14 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.21.6
4 
+Version: 1.21.7
5 5 
 Date: 2018-05-18
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
9 9 
 Suggests: RUnit, seqLogo, MotIV
10 10 
 Imports: rtracklayer, splitstackshape
11 
-Description: More than 9000 annotated position frequency matrices from 14 public sources, for multiple organisms.
11 
+Description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
13 13 
 License_is_FOSS: no
14 14 
 License_restricts_use: yes
Browse code

motifToGene refactored, now suuports c('motifDb', tfClass') sources

paul-shannon authored on 18/05/2018 22:05:19
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DESCRIPTION
History View file @ aaf4e1a
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.21.4
5 
-Date: 2018-05-10
4 
+Version: 1.21.6
5 
+Date: 2018-05-18
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

added query2(mdb, andTerms, orTerms=c(), notTerms=c())

paul-shannon authored on 10/05/2018 23:52:12
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DESCRIPTION
History View file @ 3cb31fd
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.21.3
5 
-Date: 2018-04-08
4 
+Version: 1.21.4
5 
+Date: 2018-05-10
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

added cisbp 2014 reference

paul-shannon authored on 09/04/2018 05:47:55
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DESCRIPTION
History View file @ 388ccbc
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.21.2
5 
-Date: 2018-01-31
4 
+Version: 1.21.3
5 
+Date: 2018-04-08
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

motifToGene and geneToMotif now guard against emtpy tables, ignore.cae option added

paul-shannon authored on 02/02/2018 00:04:51
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DESCRIPTION
History View file @ 68ba7eb
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.22
5 
-Date: 2018-01-23
4 
+Version: 1.21.2
5 
+Date: 2018-01-31
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

removed test_Imports.R, pkg passes CHECK

paul-shannon authored on 23/01/2018 18:14:17
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DESCRIPTION
History View file @ e2f7996
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.20
4 
+Version: 1.19.22
5 5 
 Date: 2018-01-23
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

added unit test to clarify geneToMotif results

paul-shannon authored on 23/01/2018 16:54:36
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DESCRIPTION
History View file @ 5f111ac
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@@ -1,14 +1,14 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.19
5 
-Date: 2017-12-07
4 
+Version: 1.19.20
5 
+Date: 2018-01-23
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
9 9 
 Suggests: RUnit, seqLogo, MotIV
10 10 
 Imports: rtracklayer, splitstackshape
11 
-Description: More than 8000 annotated position frequency matrices from 13 public sources, for multiple organisms.
11 
+Description: More than 9000 annotated position frequency matrices from 14 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
13 13 
 License_is_FOSS: no
14 14 
 License_restricts_use: yes
Browse code

Added jaspar 2018

Matthew Richards authored on 08/12/2017 02:17:22
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DESCRIPTION
History View file @ b7a40ef
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.18
5 
-Date: 2017-10-20
4 
+Version: 1.19.19
5 
+Date: 2017-12-07
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

Fixed labeling of cisbp motifs

Matthew Richards authored on 20/10/2017 20:45:38
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DESCRIPTION
History View file @ b6c129a
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.17
5 
-Date: 2017-10-04
4 
+Version: 1.19.18
5 
+Date: 2017-10-20
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

Removed large text files

Matthew Richards authored on 04/10/2017 22:42:47
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DESCRIPTION
History View file @ 8c4dd89
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.16
4 
+Version: 1.19.17
5 5 
 Date: 2017-10-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

string comparisons now sorted

paul-shannon authored on 04/10/2017 22:35:57
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DESCRIPTION
History View file @ 07b8ea8
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.15
4 
+Version: 1.19.16
5 5 
 Date: 2017-10-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

tracking down motif name equality bug

paul-shannon authored on 04/10/2017 22:07:08
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.14
4 
+Version: 1.19.15
5 5 
 Date: 2017-10-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

getlocale in failing test

paul-shannon authored on 04/10/2017 21:10:45
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DESCRIPTION
History View file @ e90f526
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.13
4 
+Version: 1.19.14
5 5 
 Date: 2017-10-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

documentation for geneToMotif, motifToGene, associateT...

paul-shannon authored on 04/10/2017 19:49:25
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DESCRIPTION
History View file @ 4acf0d7
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.12
4 
+Version: 1.19.13
5 5 
 Date: 2017-10-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

bumped version

paul-shannon authored on 04/10/2017 17:49:50
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DESCRIPTION
History View file @ bca83fc
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.11
5 
-Date: 2017-10-03
4 
+Version: 1.19.12
5 
+Date: 2017-10-04
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

motifToGene sidesteps regexes by grep fixed=TRUE

paul-shannon authored on 03/10/2017 18:13:41
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DESCRIPTION
History View file @ d030e74
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@@ -1,7 +1,7 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.10
4 
+Version: 1.19.11
5 5 
 Date: 2017-10-03
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Browse code

Removed large text files

Matthew Richards authored on 03/10/2017 16:42:17
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DESCRIPTION
History View file @ b7fe234
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.9
5 
-Date: 2017-09-26
4 
+Version: 1.19.10
5 
+Date: 2017-10-03
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

motif/TF mapping sources now case insensitive

paul-shannon authored on 26/09/2017 20:09:39
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DESCRIPTION
History View file @ 3b614ce
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.8
5 
-Date: 2017-09-18
4 
+Version: 1.19.9
5 
+Date: 2017-09-26
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

Fixed jaspar format spacing and updated DESCRIPTION

Matthew Richards authored on 18/09/2017 18:31:33
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DESCRIPTION
History View file @ 1f060cb
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@@ -1,14 +1,14 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.7
5 
-Date: 2017-09-12
4 
+Version: 1.19.8
5 
+Date: 2017-09-18
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
9 9 
 Suggests: RUnit, seqLogo, MotIV
10 
-Imports: rtracklayer
11 
-Description: More than 2000 annotated position frequency matrices from nine public sources, for multiple organisms.
10 
+Imports: rtracklayer, splitstackshape
11 
+Description: More than 8000 annotated position frequency matrices from 13 public sources, for multiple organisms.
12 12 
 License: Artistic-2.0 | file LICENSE
13 13 
 License_is_FOSS: no
14 14 
 License_restricts_use: yes
Browse code

now annotates to TFs properly for MotifDb and TFClass sources

paul-shannon authored on 12/09/2017 20:20:46
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DESCRIPTION
History View file @ 094b985
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.6
5 
-Date: 2017-09-07
4 
+Version: 1.19.7
5 
+Date: 2017-09-12
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

geneToMotif, motifToGene, associateTranscriptionFactors tested

paul-shannon authored on 07/09/2017 23:28:23
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DESCRIPTION
History View file @ 49ebd9d
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.3
5 
-Date: 2017-08-12
4 
+Version: 1.19.6
5 
+Date: 2017-09-07
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

roughed in data, methods and tests for mapping tf genes <--> motifs

paul-shannon authored on 13/08/2017 00:19:12
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DESCRIPTION
History View file @ 2def1ee
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.2
5 
-Date: 2017-08-01
4 
+Version: 1.19.3
5 
+Date: 2017-08-12
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

Updated unit tests to accomodate added motifs

Matthew Richards authored on 01/08/2017 16:44:49
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DESCRIPTION
History View file @ 8ff7379
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.1
5 
-Date: 2017-07-25
4 
+Version: 1.19.2
5 
+Date: 2017-08-01
6 6 
 Author: Paul Shannon, Matt Richards
7 7 
 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
8 8 
 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

bumped version number

paul-shannon authored on 25/07/2017 23:55:13
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DESCRIPTION
History View file @ dee9dc5
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@@ -1,9 +1,9 @@
1 1 
 Package: MotifDb
2 2 
 Type: Package
3 3 
 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
4 
-Version: 1.19.0
5 
-Date: 2017-03-23
6 
-Author: Paul Shannon
4 
+Version: 1.19.1
5 
+Date: 2017-07-25
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+Author: Paul Shannon, Matt Richards
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
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 Suggests: RUnit, seqLogo, MotIV
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bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 24/04/2017 19:50:57
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.18.0
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+Version: 1.19.0
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 Date: 2017-03-23
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 24/04/2017 19:25:24
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.17.1
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+Version: 1.18.0
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 Date: 2017-03-23
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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removed vignettes Makefile, bumped version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@127674 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 23/03/2017 22:10:37
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.17.0
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-Date: 2016-01-27
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+Version: 1.17.1
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+Date: 2017-03-23
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
Browse code

bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 17/10/2016 19:10:43
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1 1 
 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.16.0
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+Version: 1.17.0
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 Date: 2016-01-27
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 17/10/2016 18:45:06
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1 1 
 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.15.0
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+Version: 1.16.0
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 Date: 2016-01-27
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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bump version after creating 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 03/05/2016 21:30:44
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.14.0
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+Version: 1.15.0
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 Date: 2016-01-27
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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Bump versions prior to creation of 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 03/05/2016 21:20:18
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.13.1
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+Version: 1.14.0
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 Date: 2016-01-27
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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changed maintainer email

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@112952 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 27/01/2016 18:45:19
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.13.0
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-Date: 2015-08-28
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+Version: 1.13.1
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+Date: 2016-01-27
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 Author: Paul Shannon
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-Maintainer: Paul Shannon <pshannon@fhcrc.org>
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