1. PanomiR
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 15:35:47
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 1.4.0
3 
+Version: 1.5.0
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 15:35:47
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 1.3.0
3 
+Version: 1.4.0
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

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

J Wokaty authored on 01/11/2022 15:26:24
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 1.2.0
3 
+Version: 1.3.0
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
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 15:26:24
Showing 1 changed files
DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 1.1.2
3 
+Version: 1.2.0
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

version bump 1.1.2 in devel

Pourya Naderi authored on 17/08/2022 19:32:39
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DESCRIPTION
History View file @ 82c9e7b
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 1.1.1
3 
+Version: 1.1.2
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

version bump in devel

Pourya Naderi authored on 11/05/2022 19:46:43
Showing 1 changed files
DESCRIPTION
History View file @ f903252
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 1.1.0
3 
+Version: 1.1.1
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

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

Nitesh Turaga authored on 26/04/2022 16:21:07
Showing 1 changed files
DESCRIPTION
History View file @ 0574f78
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 1.0.0
3 
+Version: 1.1.0
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
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 16:21:07
Showing 1 changed files
DESCRIPTION
History View file @ c7e7a63
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detection of miRNAs that regulate interacting groups of pathways
3 
-Version: 0.99.8
3 
+Version: 1.0.0
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

updating vignette

Pourya Naderi authored on 04/02/2022 00:29:02
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DESCRIPTION
History View file @ 039b0f8
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 
-Title: Inferring miRNAs targeting of pathway groups
3 
-Version: 0.99.7
2 
+Title: Detection of miRNAs that regulate interacting groups of pathways
3 
+Version: 0.99.8
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
... ... 
@@ -14,8 +14,9 @@ Description: PanomiR is a package to detect miRNAs that target groups of
14 14 
     pathways from gene expression data. This package provides functionality
15 15 
     for generating pathway activity profiles, determining differentially
16 16 
     activated pathways between user-specified conditions, determining
17 
-    clusters of pathways via PCxN package, and generating miRNAs targeting
18 
-    clusters of pathways. Each function can be used on its own.
17 
+    clusters of pathways via the PCxN package, and generating miRNAs targeting
18 
+    clusters of pathways. These function can be used separately or sequentially
19 
+    to analyze RNA-Seq data.
19 20 
 License: MIT + file LICENSE
20 21 
 Encoding: UTF-8
21 22 
 RoxygenNote: 7.1.2
Browse code

Updated Vignette

Pourya Naderi authored on 31/01/2022 22:45:59
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DESCRIPTION
History View file @ ed343db
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@@ -1,12 +1,14 @@
1 1 
 Package: PanomiR
2 2 
 Title: Inferring miRNAs targeting of pathway groups
3 
-Version: 0.99.6
3 
+Version: 0.99.7
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
7 
-    person("Winston", "Hide", email = "whide@bidmc.harvard.edu",
7 
+    person("Yue Yang (Alan)", "Teo", email = "yueyang.teo@epfl.ch",
8 8 
            role = c("aut")),
9 9 
     person("Ilya", "Sytchev", email = "isytchev@hsph.harvard.edu",
10 
+           role = c("aut")),
11 
+    person("Winston", "Hide", email = "whide@bidmc.harvard.edu",
10 12 
            role = c("aut")))
11 13 
 Description: PanomiR is a package to detect miRNAs that target groups of
12 14 
     pathways from gene expression data. This package provides functionality
... ... 
@@ -19,6 +21,7 @@ Encoding: UTF-8
19 21 
 RoxygenNote: 7.1.2
20 22 
 Suggests:
21 23 
     testthat (>= 3.0.0),
24 
+    BiocStyle,
22 25 
     knitr,
23 26 
     rmarkdown
24 27 
 Config/testthat/edition: 3
Browse code

revision3

Pourya Naderi authored on 12/01/2022 16:03:39
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DESCRIPTION
History View file @ 6950996
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Inferring miRNAs targeting of pathway groups
3 
-Version: 0.99.5
3 
+Version: 0.99.6
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

rechecking bioc validation

Pourya Naderi authored on 08/01/2022 18:54:30
Showing 1 changed files
DESCRIPTION
History View file @ 8ea2ae5
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Inferring miRNAs targeting of pathway groups
3 
-Version: 0.99.4
3 
+Version: 0.99.5
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

Revision Redo2

Pourya Naderi authored on 07/01/2022 22:58:10
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DESCRIPTION
History View file @ 2f7abc8
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Inferring miRNAs targeting of pathway groups
3 
-Version: 0.99.3
3 
+Version: 0.99.4
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

Revision Redo

Pourya Naderi authored on 07/01/2022 22:26:48
Showing 1 changed files
DESCRIPTION
History View file @ 1555f16
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Inferring miRNAs targeting of pathway groups
3 
-Version: 0.99.2
3 
+Version: 0.99.3
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

Response to reviews

Pourya Naderi authored on 07/01/2022 20:56:48
Showing 1 changed files
DESCRIPTION
History View file @ e20d554
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Inferring miRNAs targeting of pathway groups
3 
-Version: 0.99.1
3 
+Version: 0.99.2
4 4 
 Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre")),
Browse code

R version

Pourya Naderi authored on 07/01/2022 17:51:48
Showing 1 changed files
DESCRIPTION
History View file @ af78a2a
... ... 
@@ -40,7 +40,7 @@ Imports:
40 40 
     withr,
41 41 
     utils
42 42 
 Depends:
43 
-    R (>= 4.1.0)
43 
+    R (>= 4.2.0)
44 44 
 URL: https://github.com/pouryany/PanomiR
45 45 
 BugReports: https://github.com/pouryany/PanomiR/issues
46 46 
 VignetteBuilder: knitr
Browse code

GSEABase feaetures

Pourya Naderi authored on 07/01/2022 03:27:44
Showing 1 changed files
DESCRIPTION
History View file @ a80b31d
... ... 
@@ -1,9 +1,13 @@
1 1 
 Package: PanomiR
2 
-Title: Detect miRNAs That Target Groups of Pathways From Gene Expression Data
2 
+Title: Inferring miRNAs targeting of pathway groups
3 3 
 Version: 0.99.1
4 
-Authors@R:
4 
+Authors@R: c(
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 
-           role = c("aut", "cre"))
6 
+           role = c("aut", "cre")),
7 
+    person("Winston", "Hide", email = "whide@bidmc.harvard.edu",
8 
+           role = c("aut")),
9 
+    person("Ilya", "Sytchev", email = "isytchev@hsph.harvard.edu",
10 
+           role = c("aut")))
7 11 
 Description: PanomiR is a package to detect miRNAs that target groups of
8 12 
     pathways from gene expression data. This package provides functionality
9 13 
     for generating pathway activity profiles, determining differentially
... ... 
@@ -23,6 +27,7 @@ Imports:
23 27 
     clusterProfiler,
24 28 
     dplyr,
25 29 
     forcats,
30 
+    GSEABase,
26 31 
     igraph,
27 32 
     limma,
28 33 
     metap,
Browse code

replacing pipes

Pourya Naderi authored on 03/01/2022 20:17:20
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DESCRIPTION
History View file @ 68d7f24
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@@ -25,7 +25,6 @@ Imports:
25 25 
     forcats,
26 26 
     igraph,
27 27 
     limma,
28 
-    magrittr,
29 28 
     metap,
30 29 
     org.Hs.eg.db,
31 30 
     parallel,
Browse code

Addressing #79 on vignettes

Pourya Naderi authored on 14/12/2021 14:43:25
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DESCRIPTION
History View file @ 451ca36
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
2 2 
 Title: Detect miRNAs That Target Groups of Pathways From Gene Expression Data
3 
-Version: 0.99.0
3 
+Version: 0.99.1
4 4 
 Authors@R:
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre"))
Browse code

DESCRIPTION EDIT

Pourya Naderi authored on 06/12/2021 16:16:27
Showing 1 changed files
DESCRIPTION
History View file @ 5c2039f
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@@ -18,13 +18,7 @@ Suggests:
18 18 
     knitr,
19 19 
     rmarkdown
20 20 
 Config/testthat/edition: 3
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-biocViews:
22 
-    GeneExpression,
23 
-    GeneSetEnrichment,
24 
-    GeneTarget,
25 
-    miRNA,
26 
-    NetworkEnrichment,
27 
-    Pathways
21 
+biocViews: GeneExpression, GeneSetEnrichment, GeneTarget, miRNA, Pathways
28 22 
 Imports:
29 23 
     clusterProfiler,
30 24 
     dplyr,
Browse code

DESCRIPTION Depends to R 4.1.0

Pourya Naderi authored on 06/12/2021 14:33:17
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DESCRIPTION
History View file @ 6d8142d
... ... 
@@ -42,7 +42,7 @@ Imports:
42 42 
     withr,
43 43 
     utils
44 44 
 Depends:
45 
-    R (>= 4.0.0)
45 
+    R (>= 4.1.0)
46 46 
 URL: https://github.com/pouryany/PanomiR
47 47 
 BugReports: https://github.com/pouryany/PanomiR/issues
48 48 
 VignetteBuilder: knitr
Browse code

Rolling DESCRIPTION Depends to R 4.0.0

Pourya Naderi authored on 06/12/2021 00:45:38
Showing 1 changed files
DESCRIPTION
History View file @ 4a932be
... ... 
@@ -42,7 +42,7 @@ Imports:
42 42 
     withr,
43 43 
     utils
44 44 
 Depends:
45 
-    R (>= 4.2.0)
45 
+    R (>= 4.0.0)
46 46 
 URL: https://github.com/pouryany/PanomiR
47 47 
 BugReports: https://github.com/pouryany/PanomiR/issues
48 48 
 VignetteBuilder: knitr
Browse code

checks R 4.2

Pourya Naderi authored on 05/12/2021 17:32:56
Showing 1 changed files
DESCRIPTION
History View file @ d8c0361
... ... 
@@ -42,7 +42,7 @@ Imports:
42 42 
     withr,
43 43 
     utils
44 44 
 Depends:
45 
-    R (>= 4.1.0)
45 
+    R (>= 4.2.0)
46 46 
 URL: https://github.com/pouryany/PanomiR
47 47 
 BugReports: https://github.com/pouryany/PanomiR/issues
48 48 
 VignetteBuilder: knitr
Browse code

DESCRIPTION edit

Pourya Naderi authored on 03/12/2021 22:37:19
Showing 1 changed files
DESCRIPTION
History View file @ 9af8d01
... ... 
@@ -16,9 +16,7 @@ RoxygenNote: 7.1.2
16 16 
 Suggests:
17 17 
     testthat (>= 3.0.0),
18 18 
     knitr,
19 
-    rmarkdown,
20 
-    pcxn,
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-    pcxnData
19 
+    rmarkdown
22 20 
 Config/testthat/edition: 3
23 21 
 biocViews:
24 22 
     GeneExpression,
... ... 
@@ -45,4 +43,6 @@ Imports:
45 43 
     utils
46 44 
 Depends:
47 45 
     R (>= 4.1.0)
46 
+URL: https://github.com/pouryany/PanomiR
47 
+BugReports: https://github.com/pouryany/PanomiR/issues
48 48 
 VignetteBuilder: knitr
Browse code

Editing DESCRIPTION, suggets. Biocviews

Pourya Naderi authored on 02/12/2021 16:23:14
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DESCRIPTION
History View file @ 5bfa6da
... ... 
@@ -16,11 +16,16 @@ RoxygenNote: 7.1.2
16 16 
 Suggests:
17 17 
     testthat (>= 3.0.0),
18 18 
     knitr,
19 
-    rmarkdown
19 
+    rmarkdown,
20 
+    pcxn,
21 
+    pcxnData
20 22 
 Config/testthat/edition: 3
21 23 
 biocViews:
22 24 
     GeneExpression,
25 
+    GeneSetEnrichment,
23 26 
     GeneTarget,
27 
+    miRNA,
28 
+    NetworkEnrichment,
24 29 
     Pathways
25 30 
 Imports:
26 31 
     clusterProfiler,
Browse code

ClusterProfiler installation

Pourya Naderi authored on 01/12/2021 22:08:41
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DESCRIPTION
History View file @ e691f7e
... ... 
@@ -23,7 +23,7 @@ biocViews:
23 23 
     GeneTarget,
24 24 
     Pathways
25 25 
 Imports:
26 
-    AnnotationDbi,
26 
+    clusterProfiler,
27 27 
     dplyr,
28 28 
     forcats,
29 29 
     igraph,
... ... 
@@ -37,8 +37,6 @@ Imports:
37 37 
     rlang,
38 38 
     tibble,
39 39 
     withr,
40 
-    DOSE,
41 
-    clusterProfiler,
42 40 
     utils
43 41 
 Depends:
44 42 
     R (>= 4.1.0)
Browse code

ClusterProfiler installation

Pourya Naderi authored on 01/12/2021 21:58:59
Showing 1 changed files
DESCRIPTION
History View file @ c88b6e5
... ... 
@@ -23,7 +23,7 @@ biocViews:
23 23 
     GeneTarget,
24 24 
     Pathways
25 25 
 Imports:
26 
-    clusterProfiler,
26 
+    AnnotationDbi,
27 27 
     dplyr,
28 28 
     forcats,
29 29 
     igraph,
... ... 
@@ -37,6 +37,8 @@ Imports:
37 37 
     rlang,
38 38 
     tibble,
39 39 
     withr,
40 
+    DOSE,
41 
+    clusterProfiler,
40 42 
     utils
41 43 
 Depends:
42 44 
     R (>= 4.1.0)
Browse code

DESC edit

Pourya Naderi authored on 01/12/2021 21:52:56
Showing 1 changed files
DESCRIPTION
History View file @ 389ff36
... ... 
@@ -5,7 +5,11 @@ Authors@R:
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre"))
7 7 
 Description: PanomiR is a package to detect miRNAs that target groups of
8 
-    pathways from gene expression data.
8 
+    pathways from gene expression data. This package provides functionality
9 
+    for generating pathway activity profiles, determining differentially
10 
+    activated pathways between user-specified conditions, determining
11 
+    clusters of pathways via PCxN package, and generating miRNAs targeting
12 
+    clusters of pathways. Each function can be used on its own.
9 13 
 License: MIT + file LICENSE
10 14 
 Encoding: UTF-8
11 15 
 RoxygenNote: 7.1.2
Browse code

test description removal

Pourya Naderi authored on 01/12/2021 21:41:54
Showing 1 changed files
DESCRIPTION
History View file @ 6949825
... ... 
@@ -5,10 +5,7 @@ Authors@R:
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre"))
7 7 
 Description: PanomiR is a package to detect miRNAs that target groups of
8 
-    pathways from gene expression data. This package provides functionalityfor generating pathway activity profiles, determining differentially
9 
-    activated pathways between user-specified conditions, determining
10 
-    clusters of pathways via PCxN package, and generating miRNAs targeting
11 
-    clusters of pathways. Each function can be used on its own
8 
+    pathways from gene expression data.
12 9 
 License: MIT + file LICENSE
13 10 
 Encoding: UTF-8
14 11 
 RoxygenNote: 7.1.2
Browse code

typo

Pourya Naderi authored on 01/12/2021 21:38:25
Showing 1 changed files
DESCRIPTION
History View file @ bbdefc7
... ... 
@@ -5,11 +5,10 @@ Authors@R:
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre"))
7 7 
 Description: PanomiR is a package to detect miRNAs that target groups of
8 
-    pathways from gene expression data. This package provides functionality
9 
-    for generating pathway activity profiles, determining differentially
8 
+    pathways from gene expression data. This package provides functionalityfor generating pathway activity profiles, determining differentially
10 9 
     activated pathways between user-specified conditions, determining
11 10 
     clusters of pathways via PCxN package, and generating miRNAs targeting
12 
-    clusters of pathways. Each function can be used on its own.
11 
+    clusters of pathways. Each function can be used on its own
13 12 
 License: MIT + file LICENSE
14 13 
 Encoding: UTF-8
15 14 
 RoxygenNote: 7.1.2
Browse code

no BiocCheck Err, lint

Pourya Naderi authored on 01/12/2021 21:33:38
Showing 1 changed files
DESCRIPTION
History View file @ 4e5ec5e
... ... 
@@ -5,7 +5,11 @@ Authors@R:
5 5 
     person("Pourya", "Naderi", email = "pouryany@gmail.com",
6 6 
            role = c("aut", "cre"))
7 7 
 Description: PanomiR is a package to detect miRNAs that target groups of
8 
-    pathways from gene expression data.
8 
+    pathways from gene expression data. This package provides functionality
9 
+    for generating pathway activity profiles, determining differentially
10 
+    activated pathways between user-specified conditions, determining
11 
+    clusters of pathways via PCxN package, and generating miRNAs targeting
12 
+    clusters of pathways. Each function can be used on its own.
9 13 
 License: MIT + file LICENSE
10 14 
 Encoding: UTF-8
11 15 
 RoxygenNote: 7.1.2
Browse code

setting seed withr

Pourya Naderi authored on 01/12/2021 14:08:58
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DESCRIPTION
History View file @ d1068d4
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@@ -32,6 +32,7 @@ Imports:
32 32 
     RColorBrewer,
33 33 
     rlang,
34 34 
     tibble,
35 
+    withr,
35 36 
     utils
36 37 
 Depends:
37 38 
     R (>= 4.1.0)
Browse code

hotfix

Former-commit-id: 26f6f2cb747b96b15e3429ed3e6b19c428398ae4 [formerly 1d25fbac9e5e145d30f183d2802e916960397d56] [formerly 6e6e2bf3cb86b11c1fea6b451315b44e3186687d [formerly 8730324eb033b6e00665ce86081a2c018c3c25a4]]
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Former-commit-id: 1fcf24015058a6b37c102ede667706c772b6c65d

Pourya Naderi authored on 19/11/2021 16:51:35
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DESCRIPTION
History View file @ 9bdcc96
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@@ -36,4 +36,3 @@ Imports:
36 36 
 Depends:
37 37 
     R (>= 4.1.0)
38 38 
 VignetteBuilder: knitr
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-
Browse code

Merge branch 'main' into add_vignette

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Pourya Naderi authored on 19/11/2021 16:41:44 • GitHub committed on 19/11/2021 16:41:44
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adding vignette directory

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Pourya Naderi authored on 18/11/2021 20:43:22
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DESCRIPTION
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@@ -10,7 +10,9 @@ License: MIT + file LICENSE
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 Encoding: UTF-8
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 RoxygenNote: 7.1.2
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-    testthat (>= 3.0.0)
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+    testthat (>= 3.0.0),
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+    knitr,
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+    rmarkdown
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 biocViews:
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     GeneExpression,
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     utils
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 Depends:
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     R (>= 2.10)
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+VignetteBuilder: knitr
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Update R version dependency

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Ilya Sytchev authored on 18/11/2021 16:01:13
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     tibble,
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 Depends:
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Add suggested biocViews

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Ilya Sytchev authored on 17/11/2021 23:19:04
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@@ -13,7 +13,9 @@ Suggests:
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     testthat (>= 3.0.0)
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 biocViews:
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+    GeneExpression,
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     dplyr,
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Fix data documentation

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Ilya Sytchev authored on 17/11/2021 23:00:23
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DESCRIPTION
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@@ -8,14 +8,13 @@ Description: PanomiR is a package to detect miRNAs that target groups of
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     pathways from gene expression data.
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 License: MIT + file LICENSE
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     testthat (>= 3.0.0)
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     clusterProfiler,
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     forcats,
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     rlang,
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     tibble,
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     R (>= 2.10)
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Update version for Bioc submission and add biocViews

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Ilya Sytchev authored on 17/11/2021 21:25:30
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: PanomiR
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 Title: Detect miRNAs That Target Groups of Pathways From Gene Expression Data
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-Version: 0.0.0.9000
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+Version: 0.99.0
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 Authors@R:
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     person("Pourya", "Naderi", email = "pouryany@gmail.com",
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            role = c("aut", "cre"))
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     pathways from gene expression data.
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     testthat (>= 3.0.0)
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 Config/testthat/edition: 3
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 biocViews:
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+    GeneExpression
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     clusterProfiler,
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     dplyr,
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Remove unused import and correct alphabetical order

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Ilya Sytchev authored on 16/11/2021 22:03:11
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     dplyr,
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     forcats,
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     igraph,
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     limma,
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     magrittr,
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     org.Hs.eg.db,
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     parallel,
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Fix undefined references to globals

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Ilya Sytchev authored on 15/11/2021 23:23:30
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     igraph,
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     metap,
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     limma,
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+    magrittr,
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     org.Hs.eg.db,
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 Depends:
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     R (>= 2.10)
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Enable data file compression using bzip2

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Ilya Sytchev authored on 10/11/2021 21:53:10
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DESCRIPTION
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@@ -9,6 +9,7 @@ Description: PanomiR is a package to detect miRNAs that target groups of
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 License: MIT + file LICENSE
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+LazyDataCompression: bzip2
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 RoxygenNote: 7.1.2
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     testthat (>= 3.0.0)
Browse code

Changing RDS to Rdata, keeping necessary files. Fix #24 Fix #25

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Pourya Naderi authored on 10/11/2021 20:52:57
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DESCRIPTION
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     preprocessCore,
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     RColorBrewer,
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     tibble
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+Depends:
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+    R (>= 2.10)
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Add forcats to satisfy undeclared import

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Ilya Sytchev authored on 05/11/2021 19:26:39
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DESCRIPTION
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@@ -17,6 +17,7 @@ biocViews:
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 Imports:
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     clusterProfiler,
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     dplyr,
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     igraph,
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     metap,
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Declare imports

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Ilya Sytchev authored on 21/10/2021 00:41:00
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DESCRIPTION
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 Suggests:
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+biocViews:
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Add test infrastructure

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Ilya Sytchev authored on 20/10/2021 19:16:37
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DESCRIPTION
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@@ -10,3 +10,6 @@ License: MIT + file LICENSE
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 Encoding: UTF-8
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Create initial documentation and remove unnecessary code

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Ilya Sytchev authored on 19/10/2021 22:50:30
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DESCRIPTION
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Add description, license, and R Studio project file

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Ilya Sytchev authored on 18/10/2021 22:55:36
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DESCRIPTION
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+Package: PanomiR
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+Title: Detect miRNAs That Target Groups of Pathways From Gene Expression Data
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+Version: 0.0.0.9000
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+Authors@R:
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+    person("Pourya", "Naderi", email = "pouryany@gmail.com",
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+           role = c("aut", "cre"))
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+Description: PanomiR is a package to detect miRNAs that target groups of
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+    pathways from gene expression data.
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+License: MIT + file LICENSE
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+Encoding: UTF-8
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+LazyData: true