1. easier
  2. DESCRIPTION
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bump x.y.z version to odd y following creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 15:06:43
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 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.12.0
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+Version: 1.13.0
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 Authors@R:
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     c(
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         person(
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bump x.y.z version to even y prior to creation of RELEASE_3_20 branch

J Wokaty authored on 29/10/2024 15:06:43
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 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.11.0
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+Version: 1.12.0
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 Authors@R:
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     c(
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         person(
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bump x.y.z version to odd y following creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 15:39:08
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 Package: easier
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 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.10.0
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+Version: 1.11.0
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 Authors@R:
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     c(
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         person(
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bump x.y.z version to even y prior to creation of RELEASE_3_19 branch

J Wokaty authored on 30/04/2024 15:39:08
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 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.9.0
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+Version: 1.10.0
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 Authors@R:
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     c(
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         person(
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bump x.y.z version to odd y following creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 15:38:21
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 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.8.0
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+Version: 1.9.0
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 Authors@R:
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     c(
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         person(
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bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 15:38:21
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1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
3 
-Version: 1.7.1
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+Version: 1.8.0
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 Authors@R:
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     c(
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         person(
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fixing LR pairs NA in vignette

olapuente authored on 06/07/2023 13:50:51
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DESCRIPTION
History View file @ 1d47e44
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@@ -63,7 +63,7 @@ Imports:
63 63 
     magrittr,
64 64 
     coin
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 Suggests:
66 
-    knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
66 
+    knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper
67 67 
 biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression, ExperimentHubSoftware
68 68 
 VignetteBuilder: knitr
69 69 
 Encoding: UTF-8
Browse code

Merge branch 'master' of github.com:olapuentesantana/easier

olapuente authored on 06/07/2023 13:45:50
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Bumped devel to 1.7.1

olapuente authored on 06/07/2023 13:44:27
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DESCRIPTION
History View file @ c2fe6d7
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
3 
-Version: 1.7.0
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+Version: 1.7.1
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 Authors@R:
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     c(
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         person(
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Merge branch 'master' into RELEASE_3_17

olapuentesantana authored on 26/05/2023 14:56:42 • GitHub committed on 26/05/2023 14:56:42
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use of decoupleR:run_viper instead of dorothea:run_viper

olapuente authored on 24/05/2023 15:40:59
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DESCRIPTION
History View file @ 6b5abf1
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@@ -41,6 +41,7 @@ Imports:
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     progeny,
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     easierData,
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     dorothea (>= 1.6.0),
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+    decoupleR,
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     quantiseqr,
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     ROCR,
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     grDevices,
... ... 
@@ -51,12 +52,15 @@ Imports:
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     DESeq2,
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     utils,
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     dplyr,
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+    tidyr,
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+    tibble,
54 57 
     matrixStats,
55 58 
     rlang,
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     BiocParallel,
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     reshape2,
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     rstatix,
59 62 
     ggrepel,
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+    magrittr,
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     coin
61 65 
 Suggests:
62 66 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
... ... 
@@ -64,5 +68,5 @@ biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, Ge
64 68 
 VignetteBuilder: knitr
65 69 
 Encoding: UTF-8
66 70 
 Roxygen: list(markdown = TRUE)
67 
-RoxygenNote: 7.2.1
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+RoxygenNote: 7.2.3
68 72 
 Config/testthat/edition: 3
Browse code

Modified version number z

olapuente authored on 19/05/2023 08:20:50
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DESCRIPTION
History View file @ 554f31b
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
3 
-Version: 1.6.1
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+Version: 1.6.2
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 Authors@R:
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     c(
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         person(
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version bump z=1

olapuente authored on 16/05/2023 11:19:42
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DESCRIPTION
History View file @ 143cff1
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1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
3 
-Version: 1.6.0
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+Version: 1.6.1
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 Authors@R:
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     c(
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         person(
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prepare next devel

olapuente authored on 16/05/2023 11:18:11
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DESCRIPTION
History View file @ 4be6fc8
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.3.2
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+Version: 1.7.0
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 Authors@R:
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     c(
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         person(
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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 15:34:46
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DESCRIPTION
History View file @ d960729
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@@ -1,6 +1,6 @@
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 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.5.0
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+Version: 1.6.0
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 Authors@R:
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     c(
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         person(
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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 15:26:08
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DESCRIPTION
History View file @ 5c4616c
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@@ -1,6 +1,6 @@
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 Package: easier
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 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.4.0
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 Authors@R:
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     c(
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         person(
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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 15:26:08
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DESCRIPTION
History View file @ 20ef4de
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.3.2
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+Version: 1.4.0
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 Authors@R:
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     c(
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         person(
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hacky solution @importFrom coin pvalue

olapuente authored on 13/10/2022 20:53:16
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DESCRIPTION
History View file @ ed9c089
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.3.1
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+Version: 1.3.2
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 Authors@R:
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     c(
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bump to z+1 to trigger new build

olapuente authored on 10/10/2022 14:41:33
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DESCRIPTION
History View file @ 9b92bc0
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.3.0
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+Version: 1.3.1
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 Authors@R:
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     c(
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         person(
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coin should be an import

olapuente authored on 06/10/2022 15:45:53
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DESCRIPTION
History View file @ bc15ab8
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@@ -56,7 +56,8 @@ Imports:
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     BiocParallel,
57 57 
     reshape2,
58 58 
     rstatix,
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-    ggrepel
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+    ggrepel,
60 
+    coin
60 61 
 Suggests:
61 62 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
62 63 
 biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression, ExperimentHubSoftware
Browse code

Merge branch 'master' of git.bioconductor.org:packages/easier

olapuente authored on 04/10/2022 22:01:22
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Version bumping prior to next release

olapuente authored on 04/10/2022 21:57:09
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DESCRIPTION
History View file @ f7e4a14
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
3 
-Version: 1.1.0
3 
+Version: 1.3.1
4 4 
 Authors@R:
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     c(
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         person(
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Passing BiocCheck

olapuente authored on 04/10/2022 21:25:26
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DESCRIPTION
History View file @ 4587a73
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@@ -36,7 +36,7 @@ Description: This package provides a workflow for the use of EaSIeR tool, develo
36 36 
              form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.
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 License: MIT + file LICENSE
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 Depends:
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-    R (>= 4.1.0)
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+    R (>= 4.2.0)
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 Imports:
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     progeny,
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     easierData,
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@@ -56,8 +56,7 @@ Imports:
56 56 
     BiocParallel,
57 57 
     reshape2,
58 58 
     rstatix,
59 
-    ggrepel,
60 
-    coin
59 
+    ggrepel
61 60 
 Suggests:
62 61 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
63 62 
 biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression, ExperimentHubSoftware
Browse code

Refine documentation with roxygen

olapuente authored on 04/10/2022 15:06:31
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DESCRIPTION
History View file @ a929573
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@@ -47,7 +47,7 @@ Imports:
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     stats,
48 48 
     graphics,
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     ggplot2,
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-    grid,
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+    ggpubr,
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     DESeq2,
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     utils,
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     dplyr,
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@@ -64,5 +64,5 @@ biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, Ge
64 64 
 VignetteBuilder: knitr
65 65 
 Encoding: UTF-8
66 66 
 Roxygen: list(markdown = TRUE)
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-RoxygenNote: 7.1.2
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+RoxygenNote: 7.2.1
68 68 
 Config/testthat/edition: 3
Browse code

Removed computation of cell type fractions that depend on remotes

olapuente authored on 04/10/2022 10:28:23
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DESCRIPTION
History View file @ 00b9f25
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@@ -40,9 +40,8 @@ Depends:
40 40 
 Imports:
41 41 
     progeny,
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     easierData,
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-    dorothea (>= 1.0.0),
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+    dorothea (>= 1.6.0),
44 44 
     quantiseqr,
45 
-    immunedeconv,
46 45 
     ROCR,
47 46 
     grDevices,
48 47 
     stats,
Browse code

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

Nitesh Turaga authored on 26/04/2022 16:19:59
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DESCRIPTION
History View file @ 038241a
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
3 
-Version: 1.2.0
3 
+Version: 1.3.0
4 4 
 Authors@R:
5 5 
     c(
6 6 
         person(
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 16:19:59
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DESCRIPTION
History View file @ b7e747a
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.1.0
3 
+Version: 1.2.0
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 Authors@R:
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     c(
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         person(
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added custom discretize function used RIR signature

olapuente authored on 25/02/2022 11:44:53
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DESCRIPTION
History View file @ 3d10356
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@@ -54,7 +54,6 @@ Imports:
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     dplyr,
55 55 
     matrixStats,
56 56 
     rlang,
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-    arules,
58 57 
     BiocParallel,
59 58 
     reshape2,
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     rstatix,
Browse code

added cell fractiosn for cafs and endo using epic

olapuente authored on 25/02/2022 10:40:03
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DESCRIPTION
History View file @ 249dd33
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@@ -42,6 +42,7 @@ Imports:
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     easierData,
43 43 
     dorothea (>= 1.0.0),
44 44 
     quantiseqr,
45 
+    immunedeconv,
45 46 
     ROCR,
46 47 
     grDevices,
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     stats,
Browse code

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

Nitesh Turaga authored on 26/10/2021 17:14:15
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DESCRIPTION
History View file @ abf69a6
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 1.0.0
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+Version: 1.1.0
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 Authors@R:
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     c(
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         person(
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 17:14:15
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DESCRIPTION
History View file @ efb058c
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.12
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+Version: 1.0.0
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 Authors@R:
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     c(
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         person(
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bump version, 0.99.12

olapuente authored on 21/10/2021 22:37:39
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DESCRIPTION
History View file @ 51d9cd8
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.11
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+Version: 0.99.12
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 Authors@R:
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     c(
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bump version, 0.99.11

olapuente authored on 21/10/2021 22:03:50
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DESCRIPTION
History View file @ f0e4f39
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.10
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+Version: 0.99.11
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 Authors@R:
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     c(
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Browse code

Added coin package to Imports

olapuente authored on 21/10/2021 15:30:38
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DESCRIPTION
History View file @ d179cc7
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@@ -57,7 +57,8 @@ Imports:
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     BiocParallel,
58 58 
     reshape2,
59 59 
     rstatix,
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-    ggrepel
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+    ggrepel,
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+    coin
61 62 
 Suggests:
62 63 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
63 64 
 biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression, ExperimentHubSoftware
Browse code

bump version, 0.99.10

olapuente authored on 18/10/2021 12:47:05
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DESCRIPTION
History View file @ b388571
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.9
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+Version: 0.99.10
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 Authors@R:
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     c(
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Browse code

bump version, 0.99.9

olapuente authored on 18/10/2021 11:54:15
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DESCRIPTION
History View file @ 1621746
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.8
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+Version: 0.99.9
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 Authors@R:
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     c(
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Browse code

bump version, 0.99.8

olapuente authored on 18/10/2021 10:44:57
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DESCRIPTION
History View file @ feed76b
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.7
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+Version: 0.99.8
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 Authors@R:
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     c(
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Browse code

version bump, 0.99.7

olapuente authored on 18/10/2021 08:27:26
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DESCRIPTION
History View file @ a9ad414
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.6
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+Version: 0.99.7
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 Authors@R:
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     c(
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version bump, 0.99.6

olapuente authored on 18/10/2021 07:57:10
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DESCRIPTION
History View file @ bbc3cb1
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.5
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+Version: 0.99.6
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     c(
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Browse code

Version bump, 0.99.5

Federico Marini authored on 15/10/2021 15:14:42
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DESCRIPTION
History View file @ 9d8e544
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@@ -1,6 +1,6 @@
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 Package: easier
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 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.4
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+Version: 0.99.5
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bump to 0.99.4 version

olapuente authored on 15/10/2021 11:33:28
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DESCRIPTION
History View file @ 53f5ba2
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
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 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.3
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+Version: 0.99.4
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Browse code

bump to version 0.99.3

olapuente authored on 14/10/2021 15:27:31
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DESCRIPTION
History View file @ 9cae794
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
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 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.2
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+Version: 0.99.3
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bump to 0.99.2 version

olapuente authored on 14/10/2021 14:16:57
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DESCRIPTION
History View file @ 1dd1b6b
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.1
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+Version: 0.99.2
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 Authors@R:
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Browse code

bump version to 0.99.1

olapuente authored on 08/10/2021 13:28:05
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DESCRIPTION
History View file @ e7bc6a5
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@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
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-Version: 0.99.0
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+Version: 0.99.1
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 Authors@R:
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     c(
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         person(
Browse code

single line biocViews

olapuente authored on 01/10/2021 15:38:21
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DESCRIPTION
History View file @ 79281b5
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@@ -65,3 +65,4 @@ VignetteBuilder: knitr
65 65 
 Encoding: UTF-8
66 66 
 Roxygen: list(markdown = TRUE)
67 67 
 RoxygenNote: 7.1.2
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+Config/testthat/edition: 3
Browse code

single line biocViews

olapuente authored on 01/10/2021 15:34:04
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DESCRIPTION
History View file @ 9176f51
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@@ -60,10 +60,7 @@ Imports:
60 60 
     ggrepel
61 61 
 Suggests:
62 62 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
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-biocViews:
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-    GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment,
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-    ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression,
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-    ExperimentHubSoftware
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+biocViews: GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression, ExperimentHubSoftware
67 64 
 VignetteBuilder: knitr
68 65 
 Encoding: UTF-8
69 66 
 Roxygen: list(markdown = TRUE)
Browse code

removed space in biocViews

olapuente authored on 01/10/2021 15:28:22
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DESCRIPTION
History View file @ 040c5bd
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@@ -61,7 +61,7 @@ Imports:
61 61 
 Suggests:
62 62 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
63 63 
 biocViews:
64 
-    GeneExpression, Software, Transcription, SystemsBiology,Pathways, GeneSetEnrichment,
64 
+    GeneExpression, Software, Transcription, SystemsBiology, Pathways, GeneSetEnrichment,
65 65 
     ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression,
66 66 
     ExperimentHubSoftware
67 67 
 VignetteBuilder: knitr
Browse code

modified description to match biocViews

olapuente authored on 01/10/2021 15:15:21
Showing 1 changed files
DESCRIPTION
History View file @ 894601a
... ... 
@@ -34,6 +34,7 @@ Description: This package provides a workflow for the use of EaSIeR tool, develo
34 34 
              cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated
35 35 
              in the literature and the performance of EaSIeR predictions has been validated using independent datasets
36 36 
              form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.
37 
+License: MIT + file LICENSE
37 38 
 Depends:
38 39 
     R (>= 4.1.0)
39 40 
 Imports:
... ... 
@@ -59,12 +60,11 @@ Imports:
59 60 
     ggrepel
60 61 
 Suggests:
61 62 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
62 
-License: MIT + file LICENSE
63 
+biocViews:
64 
+    GeneExpression, Software, Transcription, SystemsBiology,Pathways, GeneSetEnrichment,
65 
+    ImmunoOncology, Epigenetics, Classification, BiomedicalInformatics, Regression,
66 
+    ExperimentHubSoftware
67 
+VignetteBuilder: knitr
63 68 
 Encoding: UTF-8
64 69 
 Roxygen: list(markdown = TRUE)
65 70 
 RoxygenNote: 7.1.2
66 
-VignetteBuilder: knitr
67 
-biocViews:
68 
-    GeneExpression, Software, Transcription, SystemsBiology,Pathways,
69 
-    GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification,
70 
-    BiomedicalInformatics, Regression, ExperimentHubSoftware
Browse code

set Version: 0.99.0

olapuente authored on 01/10/2021 13:16:26
Showing 1 changed files
DESCRIPTION
History View file @ 61bc1fa
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: easier
2 2 
 Title: Estimate Systems Immune Response from RNA-seq data
3 
-Version: 0.9.0
3 
+Version: 0.99.0
4 4 
 Authors@R:
5 5 
     c(
6 6 
         person(
Browse code

removing the `remotes` parts - actually not needed at all once the companion package is in as well

Federico Marini authored on 01/10/2021 08:14:10
Showing 1 changed files
DESCRIPTION
History View file @ 3cdd831
... ... 
@@ -56,12 +56,9 @@ Imports:
56 56 
     BiocParallel,
57 57 
     reshape2,
58 58 
     rstatix,
59 
-    ggrepel,
60 
-    remotes
59 
+    ggrepel
61 60 
 Suggests:
62 61 
     knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
63 
-Remotes:
64 
-    olapuentesantana/easierData
65 62 
 License: MIT + file LICENSE
66 63 
 Encoding: UTF-8
67 64 
 Roxygen: list(markdown = TRUE)
Browse code

changed email in the description

olapuente authored on 30/09/2021 20:01:35
Showing 1 changed files
DESCRIPTION
History View file @ a5ddb7a
... ... 
@@ -5,7 +5,7 @@ Authors@R:
5 5 
     c(
6 6 
         person(
7 7 
             given = "Oscar", family = "Lapuente-Santana", role = c("aut", "cre"),
8 
-            email = "oscar.lapuente.santana@gmail.com", comment = c(ORCID = "0000-0003-1995-8393")
8 
+            email = "o.lapuente.santana@tue.nl", comment = c(ORCID = "0000-0003-1995-8393")
9 9 
         ),
10 10 
         person(
11 11 
             given = "Federico", family = "Marini", role = "aut",
Browse code

Added dorothea (>= 1.0.0) in DESCRIPTION

olapuente authored on 29/09/2021 23:23:51
Showing 1 changed files
DESCRIPTION
History View file @ ebc328e
... ... 
@@ -39,7 +39,7 @@ Depends:
39 39 
 Imports:
40 40 
     progeny,
41 41 
     easierData,
42 
-    dorothea,
42 
+    dorothea (>= 1.0.0),
43 43 
     quantiseqr,
44 44 
     ROCR,
45 45 
     grDevices,
Browse code

Removed @ from all examples

olapuente authored on 29/09/2021 22:31:20
Showing 1 changed files
DESCRIPTION
History View file @ 25def74
... ... 
@@ -58,14 +58,14 @@ Imports:
58 58 
     rstatix,
59 59 
     ggrepel,
60 60 
     remotes
61 
+Suggests:
62 
+    knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
61 63 
 Remotes:
62 64 
     olapuentesantana/easierData
63 65 
 License: MIT + file LICENSE
64 66 
 Encoding: UTF-8
65 67 
 Roxygen: list(markdown = TRUE)
66 68 
 RoxygenNote: 7.1.2
67 
-Suggests:
68 
-    knitr, rmarkdown, BiocStyle, testthat
69 69 
 VignetteBuilder: knitr
70 70 
 biocViews:
71 71 
     GeneExpression, Software, Transcription, SystemsBiology,Pathways,
Browse code

easierData only remains in remotes

olapuente authored on 28/09/2021 11:27:07
Showing 1 changed files
DESCRIPTION
History View file @ 8f5f2cb
... ... 
@@ -59,7 +59,6 @@ Imports:
59 59 
     ggrepel,
60 60 
     remotes
61 61 
 Remotes:
62 
-    saezlab/progeny,
63 62 
     olapuentesantana/easierData
64 63 
 License: MIT + file LICENSE
65 64 
 Encoding: UTF-8
Browse code

Updating roxygen version

Federico Marini authored on 27/09/2021 11:40:27
Showing 1 changed files
DESCRIPTION
History View file @ ec558ce
... ... 
@@ -64,7 +64,7 @@ Remotes:
64 64 
 License: MIT + file LICENSE
65 65 
 Encoding: UTF-8
66 66 
 Roxygen: list(markdown = TRUE)
67 
-RoxygenNote: 7.1.1
67 
+RoxygenNote: 7.1.2
68 68 
 Suggests:
69 69 
     knitr, rmarkdown, BiocStyle, testthat
70 70 
 VignetteBuilder: knitr
Browse code

Added easierData into Imports packages list

olapuente authored on 13/09/2021 07:25:55
Showing 1 changed files
DESCRIPTION
History View file @ 428b866
... ... 
@@ -38,6 +38,7 @@ Depends:
38 38 
     R (>= 4.1.0)
39 39 
 Imports:
40 40 
     progeny,
41 
+    easierData,
41 42 
     dorothea,
42 43 
     quantiseqr,
43 44 
     ROCR,
... ... 
@@ -62,7 +63,6 @@ Remotes:
62 63 
     olapuentesantana/easierData
63 64 
 License: MIT + file LICENSE
64 65 
 Encoding: UTF-8
65 
-LazyData: true
66 66 
 Roxygen: list(markdown = TRUE)
67 67 
 RoxygenNote: 7.1.1
68 68 
 Suggests:
Browse code

Added , in remotes

olapuente authored on 13/09/2021 06:15:39
Showing 1 changed files
DESCRIPTION
History View file @ a0cab4c
... ... 
@@ -58,7 +58,7 @@ Imports:
58 58 
     ggrepel,
59 59 
     remotes
60 60 
 Remotes:
61 
-    saezlab/progeny
61 
+    saezlab/progeny,
62 62 
     olapuentesantana/easierData
63 63 
 License: MIT + file LICENSE
64 64 
 Encoding: UTF-8
Browse code

Access internal data from easierData

olapuente authored on 11/09/2021 21:15:28
Showing 1 changed files
DESCRIPTION
History View file @ 7227fa1
... ... 
@@ -56,11 +56,10 @@ Imports:
56 56 
     reshape2,
57 57 
     rstatix,
58 58 
     ggrepel,
59 
-    remotes,
60 
-    ExperimentHub,
61 
-    AnnotationHub
59 
+    remotes
62 60 
 Remotes:
63 61 
     saezlab/progeny
62 
+    olapuentesantana/easierData
64 63 
 License: MIT + file LICENSE
65 64 
 Encoding: UTF-8
66 65 
 LazyData: true
Browse code

internal data accessed using AnnotationHub, figures are returned as objects

olapuente authored on 22/07/2021 14:04:01
Showing 1 changed files
DESCRIPTION
History View file @ b3cd201
... ... 
@@ -56,8 +56,9 @@ Imports:
56 56 
     reshape2,
57 57 
     rstatix,
58 58 
     ggrepel,
59 
-    pryr,
60 
-    remotes
59 
+    remotes,
60 
+    ExperimentHub,
61 
+    AnnotationHub
61 62 
 Remotes:
62 63 
     saezlab/progeny
63 64 
 License: MIT + file LICENSE
Browse code

First draft fully working vignette

olapuente authored on 16/07/2021 09:55:22
Showing 1 changed files
DESCRIPTION
History View file @ ae661c2
... ... 
@@ -55,7 +55,9 @@ Imports:
55 55 
     BiocParallel,
56 56 
     reshape2,
57 57 
     rstatix,
58 
-    ggrepel
58 
+    ggrepel,
59 
+    pryr,
60 
+    remotes
59 61 
 Remotes:
60 62 
     saezlab/progeny
61 63 
 License: MIT + file LICENSE
Browse code

Modified name gold_standards function

olapuente authored on 07/07/2021 08:10:09
Showing 1 changed files
DESCRIPTION
History View file @ 4ceeb44
... ... 
@@ -5,7 +5,7 @@ Authors@R:
5 5 
     c(
6 6 
         person(
7 7 
             given = "Oscar", family = "Lapuente-Santana", role = c("aut", "cre"),
8 
-            email = "o.lapuente.santana@tue.nl", comment = c(ORCID = "0000-0003-1995-8393")
8 
+            email = "oscar.lapuente.santana@gmail.com", comment = c(ORCID = "0000-0003-1995-8393")
9 9 
         ),
10 10 
         person(
11 11 
             given = "Federico", family = "Marini", role = "aut",
... ... 
@@ -37,10 +37,27 @@ Description: This package provides a workflow for the use of EaSIeR tool, develo
37 37 
 Depends:
38 38 
     R (>= 4.1.0)
39 39 
 Imports:
40 
-    ROCR, grDevices, stats, graphics, ggplot2,
41 
-    progeny, dorothea, quantiseqr, grid, DESeq2,
42 
-    utils, dplyr, matrixStats, rlang, arules,
43 
-    BiocParallel, reshape2, rstatix, ggrepel
40 
+    progeny,
41 
+    dorothea,
42 
+    quantiseqr,
43 
+    ROCR,
44 
+    grDevices,
45 
+    stats,
46 
+    graphics,
47 
+    ggplot2,
48 
+    grid,
49 
+    DESeq2,
50 
+    utils,
51 
+    dplyr,
52 
+    matrixStats,
53 
+    rlang,
54 
+    arules,
55 
+    BiocParallel,
56 
+    reshape2,
57 
+    rstatix,
58 
+    ggrepel
59 
+Remotes:
60 
+    saezlab/progeny
44 61 
 License: MIT + file LICENSE
45 62 
 Encoding: UTF-8
46 63 
 LazyData: true
... ... 
@@ -50,6 +67,6 @@ Suggests:
50 67 
     knitr, rmarkdown, BiocStyle, testthat
51 68 
 VignetteBuilder: knitr
52 69 
 biocViews:
53 
-    GeneExpression, Software, Transcription, Transcriptomics,Pathways,
70 
+    GeneExpression, Software, Transcription, SystemsBiology,Pathways,
54 71 
     GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification,
55 72 
     BiomedicalInformatics, Regression, ExperimentHubSoftware
Browse code

Depends on R 4.1.0, added quantiseqr

olapuente authored on 01/07/2021 16:23:51
Showing 1 changed files
DESCRIPTION
History View file @ 986e533
... ... 
@@ -35,14 +35,12 @@ Description: This package provides a workflow for the use of EaSIeR tool, develo
35 35 
              in the literature and the performance of EaSIeR predictions has been validated using independent datasets
36 36 
              form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.
37 37 
 Depends:
38 
-    R (>= 4.0)
38 
+    R (>= 4.1.0)
39 39 
 Imports:
40 
-    progeny, ROCR, grDevices, stats, graphics, ggplot2,
41 
-    grid, DESeq2, utils, dorothea, dplyr, matrixStats,
42 
-    immunedeconv, rlang, arules, BiocParallel, reshape2,
43 
-    rstatix, ggrepel
44 
-Remotes:
45 
-    icbi-lab/immunedeconv
40 
+    ROCR, grDevices, stats, graphics, ggplot2,
41 
+    progeny, dorothea, quantiseqr, grid, DESeq2,
42 
+    utils, dplyr, matrixStats, rlang, arules,
43 
+    BiocParallel, reshape2, rstatix, ggrepel
46 44 
 License: MIT + file LICENSE
47 45 
 Encoding: UTF-8
48 46 
 LazyData: true
Browse code

Shaping vignette

olapuente authored on 16/06/2021 16:18:31
Showing 1 changed files
DESCRIPTION
History View file @ 104eecb
... ... 
@@ -13,11 +13,11 @@ Authors@R:
13 13 
         ),
14 14 
         person(
15 15 
             given = "Arsenij", family = "Ustjanzew", role = "aut",
16 
-            email = "xx@yy.zz", comment = c(ORCID = "0000-0002-1014-4521")
16 
+            email = "arsenij.ustjanzew@uni-mainz.de", comment = c(ORCID = "0000-0002-1014-4521")
17 17 
         ),
18 18 
         person(
19 19 
             given = "Francesca", family = "Finotello", role = "aut",
20 
-            email = "xx@yy.zz", comment = c(ORCID = "0000-0003-0712-4658")
20 
+            email = "francesca.finotello@i-med.ac.at", comment = c(ORCID = "0000-0003-0712-4658")
21 21 
         ),
22 22 
         person(
23 23 
             given = "Federica", family = "Eduati", role = "aut",
Browse code

Preparing data for annotationHub

olapuente authored on 16/06/2021 12:30:38
Showing 1 changed files
DESCRIPTION
History View file @ b1f0b5a
... ... 
@@ -21,7 +21,7 @@ Authors@R:
21 21 
         ),
22 22 
         person(
23 23 
             given = "Federica", family = "Eduati", role = "aut",
24 
-            email = "xx@yy.zz", comment = c(ORCID = "0000-0002-7822-3867")
24 
+            email = "f.eduati@tue.nl", comment = c(ORCID = "0000-0002-7822-3867")
25 25 
         )
26 26 
     )
27 27 
 Description: This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood
Browse code

Getting ready for annotationHub

olapuente authored on 14/06/2021 09:57:07
Showing 1 changed files
DESCRIPTION
History View file @ d943f71
... ... 
@@ -37,27 +37,10 @@ Description: This package provides a workflow for the use of EaSIeR tool, develo
37 37 
 Depends:
38 38 
     R (>= 4.0)
39 39 
 Imports:
40 
-    progeny,
41 
-    ROCR,
42 
-    grDevices,
43 
-    stats,
44 
-    graphics,
45 
-    ggplot2,
46 
-    grid,
47 
-    DESeq2,
48 
-    utils,
49 
-    dorothea,
50 
-    dplyr,
51 
-    matrixStats,
52 
-    immunedeconv,
53 
-    rlang,
54 
-    arules,
55 
-    BiocParallel,
56 
-    reshape2,
57 
-    rstatix,
58 
-    ggrepel,
59 
-    BiocGenerics,
60 
-    Biobase
40 
+    progeny, ROCR, grDevices, stats, graphics, ggplot2,
41 
+    grid, DESeq2, utils, dorothea, dplyr, matrixStats,
42 
+    immunedeconv, rlang, arules, BiocParallel, reshape2,
43 
+    rstatix, ggrepel
61 44 
 Remotes:
62 45 
     icbi-lab/immunedeconv
63 46 
 License: MIT + file LICENSE
... ... 
@@ -66,12 +49,9 @@ LazyData: true
66 49 
 Roxygen: list(markdown = TRUE)
67 50 
 RoxygenNote: 7.1.1
68 51 
 Suggests:
69 
-    knitr,
70 
-    rmarkdown,
71 
-    BiocStyle,
72 
-    testthat
52 
+    knitr, rmarkdown, BiocStyle, testthat
73 53 
 VignetteBuilder: knitr
74 54 
 biocViews:
75 55 
     GeneExpression, Software, Transcription, Transcriptomics,Pathways,
76 56 
     GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification,
77 
-    BiomedicalInformatics, Regression
57 
+    BiomedicalInformatics, Regression, ExperimentHubSoftware
Browse code

Examples completed

olapuente authored on 11/06/2021 14:31:26
Showing 1 changed files
DESCRIPTION
History View file @ babdb58
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: easier
2 
-Title: Evaluate patient immune response to ICBs through a systems approach
2 
+Title: Estimate Systems Immune Response from RNA-seq data
3 3 
 Version: 0.9.0
4 4 
 Authors@R:
5 5 
     c(
... ... 
@@ -24,14 +24,20 @@ Authors@R:
24 24 
             email = "xx@yy.zz", comment = c(ORCID = "0000-0002-7822-3867")
25 25 
         )
26 26 
     )
27 
-Description: This package allows researchers to assess patients' likelihood to respond to ICB therapies.
28 
-             A machine learning model integrates patient transcriptomics data to gain insights into the
29 
-             effect of ICBs on the patient immune response. TODO another sentence TODO.
27 
+Description: This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood
28 
+             to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq
29 
+             data with different types of prior knowledge to extract quantitative descriptors of the tumor
30 
+             microenvironment from several points of view, including composition of the immune repertoire, and
31 
+             activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained
32 
+             in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art
33 
+             hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify
34 
+             cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated
35 
+             in the literature and the performance of EaSIeR predictions has been validated using independent datasets
36 
+             form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.
30 37 
 Depends:
31 38 
     R (>= 4.0)
32 39 
 Imports:
33 40 
     progeny,
34 
-    remotes,
35 41 
     ROCR,
36 42 
     grDevices,
37 43 
     stats,
... ... 
@@ -43,7 +49,6 @@ Imports:
43 49 
     dorothea,
44 50 
     dplyr,
45 51 
     matrixStats,
46 
-    preprocessCore,
47 52 
     immunedeconv,
48 53 
     rlang,
49 54 
     arules,
Browse code

Solved checks notes

olapuente authored on 31/05/2021 06:49:08
Showing 1 changed files
DESCRIPTION
History View file @ 84c39c6
... ... 
@@ -50,7 +50,9 @@ Imports:
50 50 
     BiocParallel,
51 51 
     reshape2,
52 52 
     rstatix,
53 
-    ggrepel
53 
+    ggrepel,
54 
+    BiocGenerics,
55 
+    Biobase
54 56 
 Remotes:
55 57 
     icbi-lab/immunedeconv
56 58 
 License: MIT + file LICENSE
Browse code

Ready for pull request

olapuente authored on 24/05/2021 11:02:01
Showing 1 changed files
DESCRIPTION
History View file @ 01c4a8b
... ... 
@@ -40,7 +40,6 @@ Imports:
40 40 
     grid,
41 41 
     DESeq2,
42 42 
     utils,
43 
-    pdist,
44 43 
     dorothea,
45 44 
     dplyr,
46 45 
     matrixStats,
... ... 
@@ -48,7 +47,10 @@ Imports:
48 47 
     immunedeconv,
49 48 
     rlang,
50 49 
     arules,
51 
-    BiocParallel
50 
+    BiocParallel,
51 
+    reshape2,
52 
+    rstatix,
53 
+    ggrepel
52 54 
 Remotes:
53 55 
     icbi-lab/immunedeconv
54 56 
 License: MIT + file LICENSE
Browse code

Added parallel settings to predict_immune_response

olapuente authored on 03/03/2021 15:56:15
Showing 1 changed files
DESCRIPTION
History View file @ 7e9a1cc
... ... 
@@ -47,7 +47,8 @@ Imports:
47 47 
     preprocessCore,
48 48 
     immunedeconv,
49 49 
     rlang,
50 
-    arules
50 
+    arules,
51 
+    BiocParallel
51 52 
 Remotes:
52 53 
     icbi-lab/immunedeconv
53 54 
 License: MIT + file LICENSE
Browse code

Added orcid Oscar

olapuente authored on 19/02/2021 12:32:42
Showing 1 changed files
DESCRIPTION
History View file @ 662b396
... ... 
@@ -4,8 +4,8 @@ Version: 0.9.0
4 4 
 Authors@R:
5 5 
     c(
6 6 
         person(
7 
-            given = "Oscar", family = "Lapuente Santana", role = c("aut", "cre"),
8 
-            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
7 
+            given = "Oscar", family = "Lapuente-Santana", role = c("aut", "cre"),
8 
+            email = "o.lapuente.santana@tue.nl", comment = c(ORCID = "0000-0003-1995-8393")
9 9 
         ),
10 10 
         person(
11 11 
             given = "Federico", family = "Marini", role = "aut",
Browse code

avoiding note from ggplot-related calls, via import of .data from rlang

Federico Marini authored on 19/02/2021 11:13:30
Showing 1 changed files
DESCRIPTION
History View file @ 62d606e
... ... 
@@ -46,6 +46,7 @@ Imports:
46 46 
     matrixStats,
47 47 
     preprocessCore,
48 48 
     immunedeconv,
49 
+    rlang,
49 50 
     arules
50 51 
 Remotes:
51 52 
     icbi-lab/immunedeconv
Browse code

import fixed for vignette, removed older unused ones

Federico Marini authored on 18/02/2021 20:58:28
Showing 1 changed files
DESCRIPTION
History View file @ 58277ab
... ... 
@@ -57,6 +57,7 @@ RoxygenNote: 7.1.1
57 57 
 Suggests:
58 58 
     knitr,
59 59 
     rmarkdown,
60 
+    BiocStyle,
60 61 
     testthat
61 62 
 VignetteBuilder: knitr
62 63 
 biocViews:
Browse code

adding suggested biocViews item

Federico Marini authored on 18/02/2021 20:11:21
Showing 1 changed files
DESCRIPTION
History View file @ 6a7c965
... ... 
@@ -62,4 +62,4 @@ VignetteBuilder: knitr
62 62 
 biocViews:
63 63 
     GeneExpression, Software, Transcription, Transcriptomics,Pathways,
64 64 
     GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification,
65 
-    BiomedicalInformatics,
65 
+    BiomedicalInformatics, Regression
Browse code

Added ORCID for the ones I could find

Federico Marini authored on 12/02/2021 21:05:08
Showing 1 changed files
DESCRIPTION
History View file @ 8af30b1
... ... 
@@ -13,20 +13,22 @@ Authors@R:
13 13 
         ),
14 14 
         person(
15 15 
             given = "Arsenij", family = "Ustjanzew", role = "aut",
16 
-            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
16 
+            email = "xx@yy.zz", comment = c(ORCID = "0000-0002-1014-4521")
17 17 
         ),
18 18 
         person(
19 19 
             given = "Francesca", family = "Finotello", role = "aut",
20 
-            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
20 
+            email = "xx@yy.zz", comment = c(ORCID = "0000-0003-0712-4658")
21 21 
         ),
22 22 
         person(
23 23 
             given = "Federica", family = "Eduati", role = "aut",
24 
-            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
24 
+            email = "xx@yy.zz", comment = c(ORCID = "0000-0002-7822-3867")
25 25 
         )
26 26 
     )
27 27 
 Description: This package allows researchers to assess patients' likelihood to respond to ICB therapies.
28 28 
              A machine learning model integrates patient transcriptomics data to gain insights into the
29 29 
              effect of ICBs on the patient immune response. TODO another sentence TODO.
30 
+Depends:
31 
+    R (>= 4.0)
30 32 
 Imports:
31 33 
     progeny,
32 34 
     remotes,
Browse code

Setup framework for unit testing

Federico Marini authored on 12/02/2021 20:31:56
Showing 1 changed files
DESCRIPTION
History View file @ 85f6381
... ... 
@@ -54,10 +54,10 @@ Roxygen: list(markdown = TRUE)
54 54 
 RoxygenNote: 7.1.1
55 55 
 Suggests:
56 56 
     knitr,
57 
-    rmarkdown
57 
+    rmarkdown,
58 
+    testthat
58 59 
 VignetteBuilder: knitr
59 60 
 biocViews:
60 61 
     GeneExpression, Software, Transcription, Transcriptomics,Pathways,
61 62 
     GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification,
62 63 
     BiomedicalInformatics,
63 
-
Browse code

version to pre 1.0.0 for conformity with Bioc, added placeholders for info on all contributors, tiny imports fix

Federico Marini authored on 12/02/2021 20:28:42
Showing 1 changed files
DESCRIPTION
History View file @ 878e292
... ... 
@@ -1,16 +1,32 @@
1 1 
 Package: easier
2 2 
 Title: Evaluate patient immune response to ICBs through a systems approach
3 
-Version: 1.0.3
3 
+Version: 0.9.0
4 4 
 Authors@R:
5 
-    person(given = "First",
6 
-           family = "Last",
7 
-           role = c("aut", "cre"),
8 
-           email = "first.last@example.com",
9 
-           comment = c(ORCID = "YOUR-ORCID-ID"))
5 
+    c(
6 
+        person(
7 
+            given = "Oscar", family = "Lapuente Santana", role = c("aut", "cre"),
8 
+            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
9 
+        ),
10 
+        person(
11 
+            given = "Federico", family = "Marini", role = "aut",
12 
+            email = "marinif@uni-mainz.de", comment = c(ORCID = "0000-0003-3252-7758")
13 
+        ),
14 
+        person(
15 
+            given = "Arsenij", family = "Ustjanzew", role = "aut",
16 
+            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
17 
+        ),
18 
+        person(
19 
+            given = "Francesca", family = "Finotello", role = "aut",
20 
+            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
21 
+        ),
22 
+        person(
23 
+            given = "Federica", family = "Eduati", role = "aut",
24 
+            email = "xx@yy.zz", comment = c(ORCID = "xxxxx")
25 
+        )
26 
+    )
10 27 
 Description: This package allows researchers to assess patients' likelihood to respond to ICB therapies.
11 28 
              A machine learning model integrates patient transcriptomics data to gain insights into the
12 
-             effect of ICBs on the patient immune response.
13 
-Depends: R (>= 4.0)
29 
+             effect of ICBs on the patient immune response. TODO another sentence TODO.
14 30 
 Imports:
15 31 
     progeny,
16 32 
     remotes,
... ... 
@@ -19,11 +35,11 @@ Imports:
19 35 
     stats,
20 36 
     graphics,
21 37 
     ggplot2,
38 
+    grid,
22 39 
     DESeq2,
23 40 
     utils,
24 41 
     pdist,
25 42 
     dorothea,
26 
-    viper,
27 43 
     dplyr,
28 44 
     matrixStats,
29 45 
     preprocessCore,
... ... 
@@ -44,3 +60,4 @@ biocViews:
44 60 
     GeneExpression, Software, Transcription, Transcriptomics,Pathways,
45 61 
     GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification,
46 62 
     BiomedicalInformatics,
63 
+
Browse code

Added some preliminary biocViews

Federico Marini authored on 12/02/2021 20:27:46
Showing 1 changed files
DESCRIPTION
History View file @ de7197b
... ... 
@@ -40,3 +40,7 @@ Suggests:
40 40 
     knitr,
41 41 
     rmarkdown
42 42 
 VignetteBuilder: knitr
43 
+biocViews:
44 
+    GeneExpression, Software, Transcription, Transcriptomics,Pathways,
45 
+    GeneSetEnrichment, ImmunoOncology, Epigenetics, Classification,
46 
+    BiomedicalInformatics,
Browse code

Added vignette placeholder and setup for this to be built in the package

Federico Marini authored on 09/12/2020 22:33:14
Showing 1 changed files
DESCRIPTION
History View file @ df67ea6
... ... 
@@ -36,3 +36,7 @@ Encoding: UTF-8
36 36 
 LazyData: true
37 37 
 Roxygen: list(markdown = TRUE)
38 38 
 RoxygenNote: 7.1.1
39 
+Suggests:
40 
+    knitr,
41 
+    rmarkdown
42 
+VignetteBuilder: knitr
Browse code

immunedeconv explicitly picked from the remotes via icbi-lab/immunedeconv

Federico Marini authored on 09/12/2020 22:30:03
Showing 1 changed files
DESCRIPTION
History View file @ 5d51082
... ... 
@@ -27,7 +27,10 @@ Imports:
27 27 
     dplyr,
28 28 
     matrixStats,
29 29 
     preprocessCore,
30 
+    immunedeconv,
30 31 
     arules
32 
+Remotes:
33 
+    icbi-lab/immunedeconv
31 34 
 License: MIT + file LICENSE
32 35 
 Encoding: UTF-8
33 36 
 LazyData: true
Browse code

move around fields in DESCRIPTION

Federico Marini authored on 09/12/2020 22:26:41
Showing 1 changed files
DESCRIPTION
History View file @ 17b2787
... ... 
@@ -11,11 +11,6 @@ Description: This package allows researchers to assess patients' likelihood to r
11 11 
              A machine learning model integrates patient transcriptomics data to gain insights into the
12 12 
              effect of ICBs on the patient immune response.
13 13 
 Depends: R (>= 4.0)
14 
-License: MIT + file LICENSE
15 
-Encoding: UTF-8
16 
-LazyData: true
17 
-Roxygen: list(markdown = TRUE)
18 
-RoxygenNote: 7.1.1
19 14 
 Imports:
20 15 
     progeny,
21 16 
     remotes,
... ... 
@@ -33,3 +28,8 @@ Imports:
33 28 
     matrixStats,
34 29 
     preprocessCore,
35 30 
     arules
31 
+License: MIT + file LICENSE
32 
+Encoding: UTF-8
33 
+LazyData: true
34 
+Roxygen: list(markdown = TRUE)
35 
+RoxygenNote: 7.1.1
Browse code

Cleanup the Depends field, Imports should be fine

Federico Marini authored on 09/12/2020 22:19:59
Showing 1 changed files
DESCRIPTION
History View file @ 6caa67b
... ... 
@@ -10,7 +10,7 @@ Authors@R:
10 10 
 Description: This package allows researchers to assess patients' likelihood to respond to ICB therapies.
11 11 
              A machine learning model integrates patient transcriptomics data to gain insights into the
12 12 
              effect of ICBs on the patient immune response.
13 
-Depends: R (>= 4.0), progeny, viper, DESeq2, ROCR, ggplot2, dorothea, preprocessCore, pdist, arules
13 
+Depends: R (>= 4.0)
14 14 
 License: MIT + file LICENSE
15 15 
 Encoding: UTF-8
16 16 
 LazyData: true
... ... 
@@ -31,4 +31,5 @@ Imports:
31 31 
     viper,
32 32 
     dplyr,
33 33 
     matrixStats,
34 
-    preprocessCore
34 
+    preprocessCore,
35 
+    arules
Browse code

Added license - MIT for the time being

Federico Marini authored on 09/12/2020 22:17:25
Showing 1 changed files
DESCRIPTION
History View file @ 4194529
... ... 
@@ -11,8 +11,7 @@ Description: This package allows researchers to assess patients' likelihood to r
11 11 
              A machine learning model integrates patient transcriptomics data to gain insights into the
12 12 
              effect of ICBs on the patient immune response.
13 13 
 Depends: R (>= 4.0), progeny, viper, DESeq2, ROCR, ggplot2, dorothea, preprocessCore, pdist, arules
14 
-License: `use_mit_license()`, `use_gpl3_license()` or friends to
15 
-    pick a license
14 
+License: MIT + file LICENSE
16 15 
 Encoding: UTF-8
17 16 
 LazyData: true
18 17 
 Roxygen: list(markdown = TRUE)
Browse code

First copy of local folder

olapuente authored on 09/12/2020 11:43:13
Showing 1 changed files
DESCRIPTION
History View file @ c40071e
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,35 @@
1 
+Package: easier
2 
+Title: Evaluate patient immune response to ICBs through a systems approach
3 
+Version: 1.0.3
4 
+Authors@R:
5 
+    person(given = "First",
6 
+           family = "Last",
7 
+           role = c("aut", "cre"),
8 
+           email = "first.last@example.com",
9 
+           comment = c(ORCID = "YOUR-ORCID-ID"))
10 
+Description: This package allows researchers to assess patients' likelihood to respond to ICB therapies.
11 
+             A machine learning model integrates patient transcriptomics data to gain insights into the
12 
+             effect of ICBs on the patient immune response.
13 
+Depends: R (>= 4.0), progeny, viper, DESeq2, ROCR, ggplot2, dorothea, preprocessCore, pdist, arules
14 
+License: `use_mit_license()`, `use_gpl3_license()` or friends to
15 
+    pick a license
16 
+Encoding: UTF-8
17 
+LazyData: true
18 
+Roxygen: list(markdown = TRUE)
19 
+RoxygenNote: 7.1.1
20 
+Imports:
21 
+    progeny,
22 
+    remotes,
23 
+    ROCR,
24 
+    grDevices,
25 
+    stats,
26 
+    graphics,
27 
+    ggplot2,
28 
+    DESeq2,
29 
+    utils,
30 
+    pdist,
31 
+    dorothea,
32 
+    viper,
33 
+    dplyr,
34 
+    matrixStats,
35 
+    preprocessCore