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added new function for faster fstat null distribution estimation and bumped version

Nils Kurzawa authored on 24/11/2022 13:09:07
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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     profiles (DLPTP)
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-Version: 1.15.1
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+Version: 1.15.2
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 Authors@R: c(
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     person("Nils", "Kurzawa", email = "nilskurzawa@gmail.com", 
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 biocViews: Software, Proteomics, DataImport
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 BugReports: https://support.bioconductor.org/
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 URL: http://bioconductor.org/packages/TPP2D
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-RoxygenNote: 7.1.0
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+RoxygenNote: 7.1.2
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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   RCurl, parallel, MASS, BiocParallel, limma
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version bump

Nils Kurzawa authored on 17/11/2022 08:37:07
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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     profiles (DLPTP)
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-Version: 1.15.0
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+Version: 1.15.1
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     person("Nils", "Kurzawa", email = "nilskurzawa@gmail.com", 
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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_16 branch

J Wokaty authored on 01/11/2022 15:19:54
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.14.0
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     person("Nils", "Kurzawa", email = "nilskurzawa@gmail.com", 
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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 15:19:54
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.13.2
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+Version: 1.14.0
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 Authors@R: c(
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     person("Nils", "Kurzawa", email = "nilskurzawa@gmail.com", 
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         role = c("aut", "cre")),
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added a filtering step in data import to prevent NA entries

Nils Kurzawa authored on 29/06/2022 14:30:43
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.13.1
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     person("Nils", "Kurzawa", email = "nilskurzawa@gmail.com", 
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version bump

Nils Kurzawa authored on 10/06/2022 08:14:33
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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     profiles (DLPTP)
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-Version: 1.13.0
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         role = c("aut", "cre")),
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changed email address

Nils Kurzawa authored on 03/05/2022 13:20:38
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 Version: 1.13.0
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 Authors@R: c(
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-    person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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+    person("Nils", "Kurzawa", email = "nilskurzawa@gmail.com", 
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         role = c("aut", "cre")),
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     person("Holger", "Franken", role = c("aut")),
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     person("Simon", "Anders", role = c("aut")),
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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 15:55:55
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-Version: 1.12.0
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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 15:55:55
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-Version: 1.11.0
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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 16:51:59
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 Package: TPP2D
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-Version: 1.10.0
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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 16:51:59
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.9.1
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+Version: 1.10.0
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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         role = c("aut", "cre")),
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fixed warning induced by difference between man and roxygen code in plot2dTppFit function

Nils Kurzawa authored on 25/05/2021 13:04:27
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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_13 branch

Nitesh Turaga authored on 19/05/2021 16:43:43
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.8.0
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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 16:43:43
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.7.4
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+Version: 1.8.0
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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         role = c("aut", "cre")),
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version bump

Nils Kurzawa authored on 21/04/2021 12:07:37
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.7.3
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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added rmarkdown as suggested package

Nils Kurzawa authored on 21/04/2021 12:05:26
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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   RCurl, parallel, MASS, BiocParallel, limma
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-Suggests: knitr, testthat
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+Suggests: knitr, testthat, rmarkdown
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updated reference in vignette and optimized plots of fits

Nils Kurzawa authored on 30/11/2020 18:22:36
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.7.2
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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added more option to plot function for TPP2D fit

Nils Kurzawa authored on 30/11/2020 16:56:08
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.7.1
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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updated reference

Nils Kurzawa authored on 13/11/2020 15:15:20
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.7.0
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+Version: 1.7.1
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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_12 branch

Nitesh Turaga authored on 27/10/2020 15:46:04
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.6.0
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+Version: 1.7.0
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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_12 branch

Nitesh Turaga authored on 27/10/2020 15:46:04
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.5.11
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+Version: 1.6.0
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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         role = c("aut", "cre")),
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corrected F stat shrinkage

Nils Kurzawa authored on 28/09/2020 08:10:51
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.5.10
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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updated function to compute p-values and to visualize volcano plot

Nils Kurzawa authored on 26/08/2020 07:26:39
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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incorporated feedback from code-review into fdr functions

Nils Kurzawa authored on 04/08/2020 16:16:06
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version bumbp

Nils Kurzawa authored on 13/07/2020 11:29:18
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version bump tp 1.5.7

Nils Kurzawa authored on 08/07/2020 06:14:21
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 Package: TPP2D
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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         role = c("aut", "cre")),
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warning is printed now when to few bootstraps are specified by a user, vignette is updated including reference to cite and fixed hyperlinks to other TPP packages

Nils Kurzawa authored on 22/06/2020 09:38:06
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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revised vignette, version bump

Nils Kurzawa authored on 20/06/2020 14:46:45
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 Package: TPP2D
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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added volcano plot function, small fix in FDR function, extended vignette

Nils Kurzawa authored on 19/06/2020 15:49:26
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 Package: TPP2D
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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version bump

Nils Kurzawa authored on 16/06/2020 16:55:10
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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     profiles (DLPTP)
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+Version: 1.5.3
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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         role = c("aut", "cre")),
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updated vignette, updated roxygen version

Nils Kurzawa authored on 16/06/2020 13:25:00
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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     profiles (DLPTP)
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-Version: 1.5.1
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+Version: 1.5.2
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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 biocViews: Software, Proteomics, DataImport
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 BugReports: https://support.bioconductor.org/
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 URL: http://bioconductor.org/packages/TPP2D
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-RoxygenNote: 6.1.1
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+RoxygenNote: 7.1.0
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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   RCurl, parallel, MASS, BiocParallel, limma
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version bump

Nils Kurzawa authored on 01/06/2020 09:06:13
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 Package: TPP2D
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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_11 branch

Nitesh Turaga authored on 27/04/2020 19:27:04
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.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_11 branch

Nitesh Turaga authored on 27/04/2020 19:27:04
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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version bump

Nils Kurzawa authored on 17/04/2020 09:21:04
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 Package: TPP2D
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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bumped version

Nils Kurzawa authored on 09/04/2020 13:52:20
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 Package: TPP2D
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+Version: 1.3.15
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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added option to shrink F stat denominator using limma::squeezeVar

Nils Kurzawa authored on 09/04/2020 08:24:10
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.3.13
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 RoxygenNote: 6.1.1
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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-  RCurl, parallel, MASS, BiocParallel
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+  RCurl, parallel, MASS, BiocParallel, limma
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 Suggests: knitr, testthat
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added function to compute pEC50 at specified temperature for protein of interest

Nils Kurzawa authored on 30/03/2020 15:32:18
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 Package: TPP2D
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 Title: Detection of ligand-protein interactions from 2D thermal 
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-Version: 1.3.12
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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updated DESCRIPTION to include method name DLPTP

Nils Kurzawa authored on 28/03/2020 10:11:55
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 Package: TPP2D
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-Title: FDR-controlled analysis of 2D-TPP experiments
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+Title: Detection of ligand-protein interactions from 2D thermal 
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+    profiles (DLPTP)
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+Version: 1.3.12
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 Authors@R: c(
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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     person("Simon", "Anders", role = c("aut")),
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     person("Wolfgang", "Huber", role = c("aut")),
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     person("Mikhail M.", "Savitski", role = c("aut")))
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-Description: FDR-controlled analysis of 2D-TPP experiments by
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-  functional analysis of dose-response curves across temperatures.
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+Description: Detection of ligand-protein interactions from 2D thermal 
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+    profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP 
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+    experiments by functional analysis of dose-response curves across 
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+    temperatures.
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 License: GPL-3
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bumped package version

Nils Kurzawa authored on 26/03/2020 11:18:10
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prevented NA F statistics from being considered for FDR estimation

Nils Kurzawa authored on 19/03/2020 15:29:04
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replaced function for computing p-values, bumped version to trigger bioc build

Nils Kurzawa authored on 29/01/2020 09:22:42
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replaced function for computing p-values

Nils Kurzawa authored on 29/01/2020 09:21:15
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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 Suggests: knitr, testthat
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version bump

Nils Kurzawa authored on 26/01/2020 14:38:04
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fixed bug in removeAmbigous protein name function

Nils Kurzawa authored on 26/01/2020 14:35:00
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version bump to trigger new bioc build

Nils Kurzawa authored on 24/01/2020 14:29:34
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-Version: 1.3.5
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addressed error in windows test of fstat function

Nils Kurzawa authored on 22/01/2020 08:30:51
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bug fix: temporarily removed knitr::include_graphics to circumvent build error

Nils Kurzawa authored on 20/01/2020 20:56:24
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updated tpp2d schematic reference to fix problem with vignette build by bioc, bumped version to trigger new build

Nils Kurzawa authored on 20/01/2020 08:01:08
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-Version: 1.3.2
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bumped version to trigger bioc build

Johanna Meichsner authored on 18/01/2020 10:51:55
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added version bump to trigger new build

Nils Kurzawa authored on 17/01/2020 12:29:30
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 Package: TPP2D
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completed update to new bootstrap method based on alternative model residuals and adapted full workflow

Nils Kurzawa authored on 16/01/2020 16:11:08
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 biocViews: Software, Proteomics, DataImport
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 URL: http://bioconductor.org/packages/TPP2D
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-RoxygenNote: 6.1.1.9000
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+RoxygenNote: 6.1.1
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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 Suggests: knitr, testthat
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resolved merge conflict based on bioc versioning

Nils Kurzawa authored on 31/10/2019 09:39:36
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bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:43:35
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bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:11:40
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 Package: TPP2D
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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added alternative function for assessing FDR via kernel density derived p-values

Nils Kurzawa authored on 29/10/2019 16:15:10
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 Package: TPP2D
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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 Suggests: knitr, testthat
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removed moderate outlier function, since outlier moderation was evaluated to compromise FDR control

Nils Kurzawa authored on 16/08/2019 10:06:40
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 Package: TPP2D
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changed function to moderate outliers by introducing global score and not allowing outlier corrections on edge cocentrations

Nils Kurzawa authored on 25/06/2019 13:59:09
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added function for outlier moderation, adapted test for new boostrapping method

Nils Kurzawa authored on 17/06/2019 16:46:34
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 Authors@R: c(
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     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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         role = c("aut", "cre")),
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+    person("Holger", "Franken", role = c("aut")),
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     person("Simon", "Anders", role = c("aut")),
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     person("Wolfgang", "Huber", role = c("aut")),
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     person("Mikhail M.", "Savitski", role = c("aut")))
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changed default behavior of computeFdr() to use more stringent resampling within ms experiments and adapted depending code

Nils Kurzawa authored on 07/06/2019 11:22:32
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one more update to the README file to include installation instructions for the development version

Nils Kurzawa authored on 08/05/2019 08:39:23
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updated installation instructions in README file to use BiocManager installation

Nils Kurzawa authored on 08/05/2019 08:24:02
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set R version requirement back to 3.6

Nils Kurzawa authored on 07/05/2019 08:23:11
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 RoxygenNote: 6.1.1.9000
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-Depends: R (>= 3.5.0), stats, utils, dplyr, methods
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+Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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 Suggests: knitr, testthat
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modified DESCRIPTION to contain co-authors, carry-over detection now works with a lda model, updated NEWS file

Nils Kurzawa authored on 07/05/2019 08:21:46
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-Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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-                  role = c("aut", "cre"))
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+Version: 1.1.1
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+Authors@R: c(
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+    person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 
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+        role = c("aut", "cre")),
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+    person("Simon", "Anders", role = c("aut")),
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+    person("Wolfgang", "Huber", role = c("aut")),
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+    person("Mikhail M.", "Savitski", role = c("aut")))
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 Description: FDR-controlled analysis of 2D-TPP experiments by
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   functional analysis of dose-response curves across temperatures.
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-URL: https://github.com/nkurzaw/TPP2D
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+BugReports: https://support.bioconductor.org/
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+URL: http://bioconductor.org/packages/TPP2D
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 RoxygenNote: 6.1.1.9000
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-Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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+Depends: R (>= 3.5.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:16:29
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bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:54:15
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bumped version to 0.99.16

Nils Kurzawa authored on 29/04/2019 05:53:53
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changed @example to @examples in data.R

Nils Kurzawa authored on 24/04/2019 05:43:57
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removed secound boostrap null test to prevent error on Windows

Nils Kurzawa authored on 23/04/2019 12:22:06
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changed dataset documentation accorsing to BioC review suggestions, included possbility to resample residuals within MS experiments during null bootstrapping

Nils Kurzawa authored on 23/04/2019 07:31:37
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renamed remaining internal functions for optimization

Nils Kurzawa authored on 16/04/2019 07:24:46
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fixed R version requirement

Nils Kurzawa authored on 15/04/2019 11:44:05
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 RoxygenNote: 6.1.1.9000
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-Depends: R (>= 3.5.0), stats, utils, dplyr, methods
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made examples runs faster to meet 10min check criterium

Nils Kurzawa authored on 15/04/2019 09:30:30
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-Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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removed maintainer field and kept only Authors@R field

Nils Kurzawa authored on 15/04/2019 09:11:51
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modified bootstrap null example to run faster, added gradient to test optimization to hopefully prevent error

Nils Kurzawa authored on 15/04/2019 08:52:10
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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adressed review comments as well as possibe

Nils Kurzawa authored on 15/04/2019 08:31:14
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@@ -1,6 +1,6 @@
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.99.6
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+Version: 0.99.7
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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@@ -9,8 +9,10 @@ Description: FDR-controlled analysis of 2D-TPP experiments by
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 License: GPL-3
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 Encoding: UTF-8
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 VignetteBuilder: knitr
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-LazyData: true
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-biocViews: Proteomics, DataImport, Software
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+LazyData: false
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+biocViews: Software, Proteomics, DataImport
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+BugReports: https://github.com/nkurzaw/TPP2D
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+URL: https://github.com/nkurzaw/TPP2D
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 RoxygenNote: 6.1.1.9000
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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changed doParallel call in bootstrapNull function to hopefully run on windows re-added examples for functions using bootstrapNull function in example, bumped version to 0.99.6

Nils Kurzawa authored on 14/03/2019 10:01:57
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.99.5
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+Version: 0.99.6
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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 biocViews: Proteomics, DataImport, Software
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 RoxygenNote: 6.1.1.9000
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 Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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-Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl
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+Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 
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+  RCurl, parallel
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 Suggests: knitr, testthat
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bumped version to 0.99.5

Nils Kurzawa authored on 14/03/2019 09:30:41
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.99.4
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+Version: 0.99.5
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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updated test for competing models function to include windows optimization variability, set bootstrapNull function example to 'not run' to prevent error on windows, bumped version to 0.99.4

Nils Kurzawa authored on 14/03/2019 09:15:02
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.99.3
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+Version: 0.99.4
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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changed example for bootstrapNull function to hopefully omit error on Windows, changed fitting tests to accept different optimization results between windows and unix, bumped version to 0.99.3

Nils Kurzawa authored on 14/03/2019 08:39:33
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.99.2
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+Version: 0.99.3
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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version is now 0.99.2

Nils Kurzawa authored on 14/03/2019 07:43:29
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.99.1
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+Version: 0.99.2
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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now subscribed to bioc-mailing list, bumped version to 0.99.1 to trigger build

Nils Kurzawa authored on 14/03/2019 07:38:15
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.99.0
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+Version: 0.99.1
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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started adressing BiocCheck notes

Nils Kurzawa authored on 11/03/2019 17:18:46
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 VignetteBuilder: knitr
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 LazyData: true
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 biocViews: Proteomics, DataImport, Software
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-RoxygenNote: 6.1.0
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-Depends: R (>= 3.5.0), stats, utils, dplyr, methods
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+RoxygenNote: 6.1.1.9000
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+Depends: R (>= 3.6.0), stats, utils, dplyr, methods
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 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl
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 Suggests: knitr, testthat
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fixed citation in introduction vignette, set version number to 0.99.0 for BioC submission, added tests for fit and compute F stat functions

Nils Kurzawa authored on 06/03/2019 09:54:40
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 Package: TPP2D
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 Title: FDR-controlled analysis of 2D-TPP experiments
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-Version: 0.1.0
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+Version: 0.99.0
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 Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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resolved more visible binding problems replaced example data once more to include correct concentrations for tru positives

Nils Kurzawa authored on 04/02/2019 18:09:22
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 LazyData: true
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 biocViews: Proteomics, DataImport, Software
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 RoxygenNote: 6.1.0
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-Depends: R (>= 3.5.0), stats, utils, dplyr
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-Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr
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+Depends: R (>= 3.5.0), stats, utils, dplyr, methods
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+Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl
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 Suggests: knitr, testthat
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resolved old link to Rcpp in description file, added new example raw data to give example and test import function, added test for import function and new manuals for additional data

Nils Kurzawa authored on 01/02/2019 11:20:10
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 Depends: R (>= 3.5.0), stats, utils, dplyr
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 Suggests: knitr, testthat
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-LinkingTo: Rcpp
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more bioccheck warnings eliminated installation guide and short package description added to readme

Nils Kurzawa authored on 31/01/2019 20:16:41
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 biocViews: Proteomics, DataImport, Software
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 Depends: R (>= 3.5.0), stats, utils, dplyr
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-Imports: 
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-  Rcpp (>= 1.0.0), ggplot2, tidyr, foreach, doParallel, 
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-  openxlsx,stringr
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+Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr
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 Suggests: knitr, testthat
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 LinkingTo: Rcpp
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adressed more bioccheck warnings and notes, including removing set.seed from functions, added testthat.R file to make devtools::check runs tests

Nils Kurzawa authored on 31/01/2019 09:23:30
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@@ -5,21 +5,16 @@ Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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                   role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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 Description: FDR-controlled analysis of 2D-TPP experiments by
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-  functional modeling of dose-response curves across temperatures.
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+  functional analysis of dose-response curves across temperatures.
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 License: GPL-3
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 Encoding: UTF-8
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 VignetteBuilder: knitr
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 LazyData: true
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-biocViews: Proteomics, LigandProteinInteractions, Software
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+biocViews: Proteomics, DataImport, Software
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 RoxygenNote: 6.1.0
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 Depends: R (>= 3.5.0), stats, utils, dplyr
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 Imports: 
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-  Rcpp (>= 1.0.0),
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-  ggplot2, 
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-  tidyr, 
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-  foreach, 
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-  doParallel, 
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-  openxlsx,
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-  stringr
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-Suggests: knitr
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+  Rcpp (>= 1.0.0), ggplot2, tidyr, foreach, doParallel, 
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+  openxlsx,stringr
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+Suggests: knitr, testthat
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 LinkingTo: Rcpp
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started fixing biocCheck errors

Nils Kurzawa authored on 30/01/2019 17:04:20
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   functional modeling of dose-response curves across temperatures.
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 License: GPL-3
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 Encoding: UTF-8
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+VignetteBuilder: knitr
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 LazyData: true
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+biocViews: Proteomics, LigandProteinInteractions, Software
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 RoxygenNote: 6.1.0
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 Depends: R (>= 3.5.0), stats, utils, dplyr
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 Imports: 
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@@ -19,4 +21,5 @@ Imports:
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   doParallel, 
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   openxlsx,
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   stringr
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+Suggests: knitr
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 LinkingTo: Rcpp
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removed TPP package dependency

Nils Kurzawa authored on 25/01/2019 16:33:43
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 Encoding: UTF-8
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 LazyData: true
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 RoxygenNote: 6.1.0
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-Depends: R (>= 3.5.0), stats, dplyr, ggplot2, foreach, doParallel, TPP
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-Imports: Rcpp (>= 1.0.0)
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+Depends: R (>= 3.5.0), stats, utils, dplyr
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+Imports: 
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+  Rcpp (>= 1.0.0),
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+  ggplot2, 
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+  tidyr, 
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+  foreach, 
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+  doParallel, 
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+  openxlsx,
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+  stringr
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 LinkingTo: Rcpp
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created wrapper functions for model fitting and bootstrapping, added TPP as bioC package to travis file

Nils Kurzawa authored on 16/01/2019 17:34:25
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 Encoding: UTF-8
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 LazyData: true
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 RoxygenNote: 6.1.0
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-Depends: R (>= 3.5.0), stats, dplyr, ggplot2
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+Depends: R (>= 3.5.0), stats, dplyr, ggplot2, foreach, doParallel, TPP
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 Imports: Rcpp (>= 1.0.0)
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 LinkingTo: Rcpp
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added cpp implementation for optimization and gradient function

Nils Kurzawa authored on 14/01/2019 17:25:14
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 LazyData: true
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 RoxygenNote: 6.1.0
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 Depends: R (>= 3.5.0), stats, dplyr, ggplot2
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+Imports: Rcpp (>= 1.0.0)
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+LinkingTo: Rcpp
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added first plot functions and changed DESCRIPTION file dependency to a 'zero'-level R version

Nils Kurzawa authored on 22/12/2018 11:42:30
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 Package: TPP2D
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-Type: Package
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 Title: FDR-controlled analysis of 2D-TPP experiments
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 Version: 0.1.0
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-Author: Nils Kurzawa 
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+Authors@R: person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de",
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+                  role = c("aut", "cre"))
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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 Description: FDR-controlled analysis of 2D-TPP experiments by
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   functional modeling of dose-response curves across temperatures.
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@@ -10,4 +10,4 @@ License: GPL-3
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 Encoding: UTF-8
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 LazyData: true
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 RoxygenNote: 6.1.0
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-Depends: R (>= 3.5.1), dplyr
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+Depends: R (>= 3.5.0), stats, dplyr, ggplot2
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maded detailed description a full sentence

Nils Kurzawa authored on 19/12/2018 10:31:13
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 Author: Nils Kurzawa 
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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 Description: FDR-controlled analysis of 2D-TPP experiments by
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-  functional modeling of dose-response curves across temperatures
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+  functional modeling of dose-response curves across temperatures.
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 License: GPL-3
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 Encoding: UTF-8
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added license, dependencies and description to DESCRIPTION file

Nils Kurzawa authored on 18/12/2018 16:12:23
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 Version: 0.1.0
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 Author: Nils Kurzawa 
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 Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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-Description: More about what it does (maybe more than one line)
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-    Use four spaces when indenting paragraphs within the Description.
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-License: What license is it under?
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+Description: FDR-controlled analysis of 2D-TPP experiments by
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+  functional modeling of dose-response curves across temperatures
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+License: GPL-3
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 Encoding: UTF-8
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 LazyData: true
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 RoxygenNote: 6.1.0
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+Depends: R (>= 3.5.1), dplyr
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initial package setup and recompute signal from ratios functions including test

Nils Kurzawa authored on 18/12/2018 15:43:29
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+Package: TPP2D
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+Type: Package
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+Title: FDR-controlled analysis of 2D-TPP experiments
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+Version: 0.1.0
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+Author: Nils Kurzawa 
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+Maintainer: Nils Kurzawa <nils.kurzawa@embl.de>
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+Description: More about what it does (maybe more than one line)
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+    Use four spaces when indenting paragraphs within the Description.
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+License: What license is it under?
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+Encoding: UTF-8
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+LazyData: true
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+RoxygenNote: 6.1.0