1. nempi
  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 15:25:29
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1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 1.8.0
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+Version: 1.9.0
5 5 
 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     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 15:25:29
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DESCRIPTION
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1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.7.0
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+Version: 1.8.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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added BiocStyle to suggests

mpirkl authored on 06/04/2023 07:12:32
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DESCRIPTION
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@@ -24,7 +24,7 @@ biocViews: Software, GeneExpression, DifferentialExpression,
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 Imports: e1071, nnet, randomForest, naturalsort,
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     graphics, stats, utils, matrixStats, epiNEM
26 26 
 VignetteBuilder: knitr
27 
-Suggests: knitr, BiocGenerics, rmarkdown, RUnit
27 
+Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle
28 28 
 BugReports: https://github.com/cbg-ethz/nempi/issues
29 29 
 URL: https://github.com/cbg-ethz/nempi/
30 30 
 RoxygenNote: 7.1.1
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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 15:23:35
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 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.6.0
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+Version: 1.7.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     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 15:23:35
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DESCRIPTION
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 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.5.0
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+Version: 1.6.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     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 16:11:30
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 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.4.0
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+Version: 1.5.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     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 16:11:30
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DESCRIPTION
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 Package: nempi
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 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.3.0
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+Version: 1.4.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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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 17:05:47
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DESCRIPTION
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1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.2.0
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+Version: 1.3.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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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 17:05:47
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DESCRIPTION
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1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 1.1.1
4 
+Version: 1.2.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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added RUnit to suggests

mpirkl authored on 28/05/2021 12:55:44
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.1.0
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+Version: 1.1.1
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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@@ -24,7 +24,7 @@ biocViews: Software, GeneExpression, DifferentialExpression,
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 Imports: e1071, nnet, randomForest, naturalsort,
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     graphics, stats, utils, matrixStats, epiNEM
26 26 
 VignetteBuilder: knitr
27 
-Suggests: knitr, BiocGenerics, rmarkdown
27 
+Suggests: knitr, BiocGenerics, rmarkdown, RUnit
28 28 
 BugReports: https://github.com/cbg-ethz/nempi/issues
29 29 
 URL: https://github.com/cbg-ethz/nempi/
30 30 
 RoxygenNote: 7.1.1
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bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:58:29
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DESCRIPTION
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1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 1.0.0
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+Version: 1.1.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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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 16:58:29
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 0.99.9
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+Version: 1.0.0
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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added rmarkdown to suggest

mpirkl authored on 16/04/2021 14:20:39
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
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-Version: 0.99.8
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+Version: 0.99.9
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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@@ -24,7 +24,7 @@ biocViews: Software, GeneExpression, DifferentialExpression,
24 24 
 Imports: e1071, nnet, randomForest, naturalsort,
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     graphics, stats, utils, matrixStats, epiNEM
26 26 
 VignetteBuilder: knitr
27 
-Suggests: knitr, BiocGenerics
27 
+Suggests: knitr, BiocGenerics, rmarkdown
28 28 
 BugReports: https://github.com/cbg-ethz/nempi/issues
29 29 
 URL: https://github.com/cbg-ethz/nempi/
30 30 
 RoxygenNote: 7.1.1
Browse code

updated citation

mpirkl authored on 23/02/2021 13:04:00
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.7
4 
+Version: 0.99.8
5 5 
 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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fixed url

mpirkl authored on 08/02/2021 13:34:29
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DESCRIPTION
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1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.6
4 
+Version: 0.99.7
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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@@ -26,5 +26,5 @@ Imports: e1071, nnet, randomForest, naturalsort,
26 26 
 VignetteBuilder: knitr
27 27 
 Suggests: knitr, BiocGenerics
28 28 
 BugReports: https://github.com/cbg-ethz/nempi/issues
29 
-URL: https://github.com/cbg-ethz/bnem/
29 
+URL: https://github.com/cbg-ethz/nempi/
30 30 
 RoxygenNote: 7.1.1
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added citation

mpirkl authored on 27/01/2021 11:13:10
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@@ -1,7 +1,7 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.5
4 
+Version: 0.99.6
5 5 
 Authors@R: person("Martin", "Pirkl",
6 6 
     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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removed deprecated require; removed mnem from imports; added recommended biocViews

mpirkl authored on 08/12/2020 14:08:35
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.4
4 
+Version: 0.99.5
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 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
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     role = c("aut", "cre"))
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@@ -18,8 +18,10 @@ Encoding: UTF-8
18 18 
 LazyData: true
19 19 
 biocViews: Software, GeneExpression, DifferentialExpression,
20 20 
     DifferentialMethylation, GeneSignaling, Pathways, Network,
21 
-    Classification, NeuralNetwork, NetworkInference
22 
-Imports: mnem, e1071, nnet, randomForest, naturalsort,
21 
+    Classification, NeuralNetwork, NetworkInference, ATACSeq,
22 
+    DNASeq, RNASeq, PooledScreens, CRISPR, SingleCell,
23 
+    SystemsBiology
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+Imports: e1071, nnet, randomForest, naturalsort,
23 25 
     graphics, stats, utils, matrixStats, epiNEM
24 26 
 VignetteBuilder: knitr
25 27 
 Suggests: knitr, BiocGenerics
Browse code

fixed missing title and authors in vignette; added mnem to Depends; removed install from github instructions from vignette; added proper S3 function for plotConvergence

mpirkl authored on 08/12/2020 13:53:52
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DESCRIPTION
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@@ -1,11 +1,11 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.3
4 
+Version: 0.99.4
5 5 
 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
7 7 
     role = c("aut", "cre"))
8 
-Depends: R (>= 4.1)
8 
+Depends: R (>= 4.1), mnem
9 9 
 Description: Takes as input an incomplete perturbation
10 10 
     profile and differential gene expression in log odds and
11 11 
     infers unobserved perturbations and augments observed
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changed R dependency to 4.1

mpirkl authored on 23/11/2020 10:44:30
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DESCRIPTION
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@@ -1,11 +1,11 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.2
4 
+Version: 0.99.3
5 5 
 Authors@R: person("Martin", "Pirkl",
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     email = "martinpirkl@yahoo.de",
7 7 
     role = c("aut", "cre"))
8 
-Depends: R (>= 4.0)
8 
+Depends: R (>= 4.1)
9 9 
 Description: Takes as input an incomplete perturbation
10 10 
     profile and differential gene expression in log odds and
11 11 
     infers unobserved perturbations and augments observed
Browse code

cleaned code; added unit tests

mpirkl authored on 23/11/2020 10:22:32
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DESCRIPTION
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@@ -1,15 +1,28 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.1
5 
-Authors@R: person("Martin", "Pirkl", email = "martinpirkl@yahoo.de",role = c("aut", "cre"))
4 
+Version: 0.99.2
5 
+Authors@R: person("Martin", "Pirkl",
6 
+    email = "martinpirkl@yahoo.de",
7 
+    role = c("aut", "cre"))
6 8 
 Depends: R (>= 4.0)
7 
-Description: Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.
9 
+Description: Takes as input an incomplete perturbation
10 
+    profile and differential gene expression in log odds and
11 
+    infers unobserved perturbations and augments observed
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+    ones. The inference is done by iteratively inferring a
13 
+    network from the perturbations and inferring perturbations
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+    from the network. The network inference is done by
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+    Nested Effects Models.
8 16 
 License: GPL-3
9 17 
 Encoding: UTF-8
10 18 
 LazyData: true
11 
-biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneSignaling, Pathways, Network, Classification, NeuralNetwork, NetworkInference
12 
-Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats
19 
+biocViews: Software, GeneExpression, DifferentialExpression,
20 
+    DifferentialMethylation, GeneSignaling, Pathways, Network,
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+    Classification, NeuralNetwork, NetworkInference
22 
+Imports: mnem, e1071, nnet, randomForest, naturalsort,
23 
+    graphics, stats, utils, matrixStats, epiNEM
13 24 
 VignetteBuilder: knitr
14 
-Suggests: knitr, BiocGenerics, epiNEM
25 
+Suggests: knitr, BiocGenerics
26 
+BugReports: https://github.com/cbg-ethz/nempi/issues
27 
+URL: https://github.com/cbg-ethz/bnem/
15 28 
 RoxygenNote: 7.1.1
Browse code

added recommended biocview

mpirkl authored on 05/11/2020 08:25:38
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DESCRIPTION
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@@ -1,14 +1,14 @@
1 1 
 Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 
-Version: 0.99.0
4 
+Version: 0.99.1
5 5 
 Authors@R: person("Martin", "Pirkl", email = "martinpirkl@yahoo.de",role = c("aut", "cre"))
6 6 
 Depends: R (>= 4.0)
7 7 
 Description: Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.
8 8 
 License: GPL-3
9 9 
 Encoding: UTF-8
10 10 
 LazyData: true
11 
-biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneSignaling, Pathways, Network, Classification, NeuralNetwork
11 
+biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneSignaling, Pathways, Network, Classification, NeuralNetwork, NetworkInference
12 12 
 Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats
13 13 
 VignetteBuilder: knitr
14 14 
 Suggests: knitr, BiocGenerics, epiNEM
Browse code

updated the dependency on mnem/nem

mpirkl authored on 04/11/2020 11:52:09
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DESCRIPTION
History View file @ 538abd4
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@@ -2,11 +2,9 @@ Package: nempi
2 2 
 Type: Package
3 3 
 Title: Inferring unobserved perturbations from gene expression data
4 4 
 Version: 0.99.0
5 
-Date: 2019-30-07
6 
-Author: Martin Pirkl
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-Maintainer: Martin Pirkl <martin.pirkl@bsse.ethz.ch>
8 
-Depends: R (>= 3.6)
9 
-Description: Takes as input an incomplete perturbation profile and differential gene expression in logodds and infers unobserved perturbations and augments observed ones.
5 
+Authors@R: person("Martin", "Pirkl", email = "martinpirkl@yahoo.de",role = c("aut", "cre"))
6 
+Depends: R (>= 4.0)
7 
+Description: Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.
10 8 
 License: GPL-3
11 9 
 Encoding: UTF-8
12 10 
 LazyData: true
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@@ -14,4 +12,4 @@ biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethyla
14 12 
 Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats
15 13 
 VignetteBuilder: knitr
16 14 
 Suggests: knitr, BiocGenerics, epiNEM
17 
-RoxygenNote: 7.1.0
15 
+RoxygenNote: 7.1.1
Browse code

fixing some issues with vignette and R checks

mpirkl authored on 30/04/2020 10:53:44
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DESCRIPTION
History View file @ 2a77102
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@@ -11,7 +11,7 @@ License: GPL-3
11 11 
 Encoding: UTF-8
12 12 
 LazyData: true
13 13 
 biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneSignaling, Pathways, Network, Classification, NeuralNetwork
14 
-Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils, nem, matrixStats
14 
+Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats
15 15 
 VignetteBuilder: knitr
16 16 
 Suggests: knitr, BiocGenerics, epiNEM
17 
-RoxygenNote: 6.1.1
17 
+RoxygenNote: 7.1.0
Browse code

added suggest epinem

MartinFXP authored on 07/11/2019 09:25:15
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DESCRIPTION
History View file @ 953cda6
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@@ -13,5 +13,5 @@ LazyData: true
13 13 
 biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneSignaling, Pathways, Network, Classification, NeuralNetwork
14 14 
 Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils, nem, matrixStats
15 15 
 VignetteBuilder: knitr
16 
-Suggests: knitr, BiocGenerics
16 
+Suggests: knitr, BiocGenerics, epiNEM
17 17 
 RoxygenNote: 6.1.1
Browse code

fixes to pass checks

MartinFXP authored on 05/11/2019 10:50:33
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DESCRIPTION
History View file @ 9ee0844
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@@ -11,7 +11,7 @@ License: GPL-3
11 11 
 Encoding: UTF-8
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 LazyData: true
13 13 
 biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneSignaling, Pathways, Network, Classification, NeuralNetwork
14 
-Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils
14 
+Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils, nem, matrixStats
15 15 
 VignetteBuilder: knitr
16 16 
 Suggests: knitr, BiocGenerics
17 17 
 RoxygenNote: 6.1.1
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Init

MartinFXP authored on 02/09/2019 12:35:02
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DESCRIPTION
History View file @ bca783f
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new file mode 100644
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@@ -0,0 +1,17 @@
1 
+Package: nempi
2 
+Type: Package
3 
+Title: Inferring unobserved perturbations from gene expression data
4 
+Version: 0.99.0
5 
+Date: 2019-30-07
6 
+Author: Martin Pirkl
7 
+Maintainer: Martin Pirkl <martin.pirkl@bsse.ethz.ch>
8 
+Depends: R (>= 3.6)
9 
+Description: Takes as input an incomplete perturbation profile and differential gene expression in logodds and infers unobserved perturbations and augments observed ones.
10 
+License: GPL-3
11 
+Encoding: UTF-8
12 
+LazyData: true
13 
+biocViews: Software, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneSignaling, Pathways, Network, Classification, NeuralNetwork
14 
+Imports: mnem, e1071, nnet, randomForest, naturalsort, graphics, stats, utils
15 
+VignetteBuilder: knitr
16 
+Suggests: knitr, BiocGenerics
17 
+RoxygenNote: 6.1.1