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19 April 2025, 14:50:48 UTC
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RevisionAuthorDateMessageCommit Date
d9c4266 Marie-laure DELIGNETTE-MULLER24 July 2019, 15:48:27 UTCAdd of the possibility to plot residuals instead of fitted curves from an object of class drcfit24 July 2019, 15:48:27 UTC
201c0b2 Marie-laure DELIGNETTE-MULLER24 July 2019, 14:08:09 UTCupdating of the NEWS file24 July 2019, 14:08:09 UTC
72fa80d Marie-laure DELIGNETTE-MULLER24 July 2019, 13:57:51 UTCadd of an argument point.type in ecdfplotwithCI()24 July 2019, 13:57:51 UTC
edae419 Marie-laure DELIGNETTE-MULLER24 July 2019, 12:39:07 UTCModification of recommendations for pretreatment of metabolomic data and add of tests (testthat) for itemselect24 July 2019, 12:39:07 UTC
93f1e19 Marie-laure DELIGNETTE-MULLER23 July 2019, 16:57:57 UTCadd of a filter in itemselect on the proportion of tolerated ties for each item23 July 2019, 16:57:57 UTC
0f49865 Marie-laure DELIGNETTE-MULLER23 July 2019, 15:22:09 UTCFixing a bug in bmdcalc that was erroneously assuming y0 positive23 July 2019, 15:22:09 UTC
7d63412 Marie-laure DELIGNETTE-MULLER22 July 2019, 16:02:35 UTCFixing of a bug occuring on metabolomic data with two many imputed values (zeros imputed to non zero by hlaf minimum before log transformation) due to several solution for which for returning the dose at which the min ou the max is reached (in starting values functions)22 July 2019, 16:02:35 UTC
9b4c7d1 Marie-laure DELIGNETTE-MULLER04 July 2019, 09:32:12 UTCAdd of check for RNAseq and microarray imported data (only warning in case of potential problem)04 July 2019, 09:32:12 UTC
e66d325 Marie-laure DELIGNETTE-MULLER04 July 2019, 09:13:05 UTCminor corrections in the description and the manual04 July 2019, 09:13:05 UTC
3f5f673 Marie-laure DELIGNETTE-MULLER04 July 2019, 07:09:43 UTCsecond try to make the run of RNAseqdata.Rd below 5 seconds04 July 2019, 07:09:43 UTC
6b37c86 Marie-laure DELIGNETTE-MULLER04 July 2019, 06:08:30 UTCreduce the running time of RNAseqdata.Rd for CRAN04 July 2019, 06:08:30 UTC
df94a01 Marie-laure DELIGNETTE-MULLER04 July 2019, 06:06:33 UTCtry to fix conflict04 July 2019, 06:06:33 UTC
321c54d Marie-laure DELIGNETTE-MULLER04 July 2019, 06:05:14 UTCtry to fix conflict of versions on Gitlab Merge branch 'master' of ssh://umr5558-gitlab.univ-lyon1.fr:10022/aursiber/DRomics # Conflicts: # man/metabolomicdata.Rd # man/microarraydata.Rd04 July 2019, 06:05:14 UTC
27069d4 Marie-laure DELIGNETTE-MULLER03 July 2019, 16:16:34 UTCTry to make running time of examples acceptale for a release on CRAN03 July 2019, 16:16:34 UTC
48ae56a Aurélie Siberchicot26 June 2019, 14:26:11 UTCCorrect some misprints26 June 2019, 14:26:11 UTC
e574b33 Marie-laure DELIGNETTE-MULLER26 June 2019, 09:50:27 UTCCorection on the .Rd files, add of a smaller RNAseq data set to run in examples and tests, add of the deprecated function omicdata and complete removing of the deprecated class "omicdata"26 June 2019, 09:50:27 UTC
3abf574 Aurélie Siberchicot24 June 2019, 06:52:34 UTCUpdate the shiny app with a new tutorial24 June 2019, 06:52:34 UTC
c081ae7 Aurélie Siberchicot21 June 2019, 07:56:16 UTCCorrect a misprint in the metabolomicdata function21 June 2019, 07:56:16 UTC
be15c0e Aurélie Siberchicot21 June 2019, 07:54:02 UTCCorrect a misprint in the shiny interface21 June 2019, 07:54:02 UTC
7a8ad9a Aurélie Siberchicot21 June 2019, 07:53:33 UTCFix an error in using ggplot21 June 2019, 07:53:33 UTC
51b53fd Aurélie Siberchicot19 June 2019, 09:07:56 UTCFix some stuff in the shiny app19 June 2019, 09:07:56 UTC
6ec33ea Aurélie Siberchicot19 June 2019, 08:49:33 UTCMerge branch 'RNAseq' into 'master' RNAseq See merge request !119 June 2019, 08:49:33 UTC
a211607 Marie-laure DELIGNETTE-MULLER19 June 2019, 08:07:39 UTCBug fixed in curvesplot (aes_()) and add of comments on metabolomic pretreatment19 June 2019, 08:07:39 UTC
332fe23 Marie-laure DELIGNETTE-MULLER19 June 2019, 06:23:42 UTCMerge branch 'RNAseq' of ssh://umr5558-gitlab.univ-lyon1.fr:10022/aursiber/DRomics into RNAseq19 June 2019, 06:23:42 UTC
59ca575 Aurélie Siberchicot17 June 2019, 15:20:52 UTCUpdate text in the shiny app17 June 2019, 15:20:52 UTC
27c6efc Aurélie Siberchicot17 June 2019, 12:47:53 UTCUpdate the shiny app with the types of input data17 June 2019, 12:47:53 UTC
cf8187e Aurélie Siberchicot17 June 2019, 11:59:12 UTCCorrect ggplot calls to avoid warnings17 June 2019, 11:59:12 UTC
522af31 Marie-laure DELIGNETTE-MULLER12 June 2019, 09:57:07 UTCadd of the deprecated class omicdata so as to make our old scripts work12 June 2019, 09:57:07 UTC
0666ea0 Marie-laure DELIGNETTE-MULLER11 June 2019, 15:01:01 UTCremoving of omicdata files and add of a help file for shiny step 1 with RNAseq data (and other minor corretions)11 June 2019, 15:01:01 UTC
fa8255a Marie-laure DELIGNETTE-MULLER11 June 2019, 11:29:15 UTCreplacement by omicdata() by microarraydata() and add of RNAseqdata() and metabolomicdata()11 June 2019, 11:29:15 UTC
ad62164 Marie-laure DELIGNETTE-MULLER21 May 2019, 10:01:06 UTCFirst step for taking into account RNAseq data21 May 2019, 10:01:06 UTC
da15040 Aurélie Siberchicot19 April 2019, 12:49:13 UTCAdd R code to go further in the shiny app19 April 2019, 12:49:13 UTC
1b44c95 Aurélie Siberchicot18 April 2019, 15:25:05 UTCUpdate the shiny app which uses the new plot.bmdcalc function18 April 2019, 15:25:05 UTC
59a4eab Aurélie Siberchicot18 April 2019, 15:10:17 UTCMerge branch 'bootstrap'18 April 2019, 15:10:17 UTC
7b2f169 Aurélie Siberchicot18 April 2019, 15:01:17 UTCMerge branch 'upShinyApp'18 April 2019, 15:01:17 UTC
68ea1ec Marie-laure DELIGNETTE-MULLER18 April 2019, 14:51:57 UTCMain work on bmdboot, bmdcalc and new function curvesplot18 April 2019, 14:51:57 UTC
d41c155 Aurélie Siberchicot16 April 2019, 15:35:56 UTCAdd a panel in the shiny app, containing the R code16 April 2019, 15:35:56 UTC
e31a96f Aurélie Siberchicot16 April 2019, 13:48:56 UTCClean the code and upgrade the shiny app16 April 2019, 13:48:56 UTC
450c047 Marie-laure DELIGNETTE-MULLER02 April 2019, 14:17:02 UTCnew arguments for ecdfplotwithCI()02 April 2019, 14:17:02 UTC
fc29591 Marie-laure DELIGNETTE-MULLER12 March 2019, 15:41:18 UTCAdd of a plot function useful for exploitation of bootstrap values with annotation informations (pathways, ...) : ecdfplotwithCI()12 March 2019, 15:41:18 UTC
52b04e1 Marie-laure DELIGNETTE-MULLER12 March 2019, 13:18:08 UTCNew version of bmdboot.R and bmdboot.Rd12 March 2019, 13:18:08 UTC
1f9ae73 Marie-laure DELIGNETTE-MULLER27 February 2019, 16:32:17 UTCnew version of bmdboot and examples that works in parallel computing27 February 2019, 16:32:17 UTC
32e592f Marie-laure DELIGNETTE-MULLER27 February 2019, 11:38:14 UTCprint and plot functions for bmdboot and a help page (bmdboot.Rd)27 February 2019, 11:38:14 UTC
91ff945 Marie-laure DELIGNETTE-MULLER22 February 2019, 15:20:04 UTCversion of bmdboot with all the models (excepted log probit - not need for the moment) and a first plot function to explore the results. Need to really include it in the package now22 February 2019, 15:20:04 UTC
0dafb57 Marie-laure DELIGNETTE-MULLER22 February 2019, 12:22:40 UTCversion of bmdboot with models GP, LGP and expo22 February 2019, 12:22:40 UTC
f887918 Marie-laure DELIGNETTE-MULLER22 February 2019, 10:29:18 UTCNew version of bmdboot that works for Gauss-probit 5p and expo, and is able to manage NA and NaN values for some of the bootstrapped BMD and failure of nls to converge for some bootstrapped samples22 February 2019, 10:29:18 UTC
0af2ec0 Marie-laure DELIGNETTE-MULLER15 February 2019, 12:45:33 UTCbmdboot version only for exponential and Gauss-probit5p models15 February 2019, 12:45:33 UTC
b1f3fed Marie-laure DELIGNETTE-MULLER15 February 2019, 11:57:21 UTCnew version of bmdboot not finished and bugged for Gauss probit 5p15 February 2019, 11:57:21 UTC
7c68c61 Marie-laure DELIGNETTE-MULLER08 February 2019, 12:02:58 UTCfirst trial for bootstrap08 February 2019, 12:02:58 UTC
a2bcf4f Marie-laure DELIGNETTE-MULLER08 February 2019, 09:42:03 UTCreplacement of x/100 by xdiv100 (calculated once) in bmdcalc in order not to replicate this calculation08 February 2019, 09:42:03 UTC
437077a Aurélie Siberchicot17 January 2019, 07:56:50 UTCUpdate the shiny app: add a reference and a link to the CRAN page of the package DRomics17 January 2019, 07:56:50 UTC
510aa90 Aurélie Siberchicot09 January 2019, 14:40:07 UTCIncrement version number09 January 2019, 14:40:07 UTC
36936a5 Aurélie Siberchicot09 January 2019, 14:38:04 UTCAdd an example about the shiny app09 January 2019, 14:38:04 UTC
f48f9c0 Marie-laure DELIGNETTE-MULLER09 January 2019, 09:22:18 UTCDuplication of examples for drcfit and bmdcalc using a very small data set to put at least one runned example for each .Rd file09 January 2019, 09:22:18 UTC
d6d3025 Aurélie Siberchicot03 January 2019, 09:09:11 UTCUpdate intro file in the shiny app to test the server updating03 January 2019, 09:09:11 UTC
122d5f7 Aurélie Siberchicot03 January 2019, 09:06:53 UTCUpdate DESCRIPTION: correct DOI reference03 January 2019, 09:06:53 UTC
96dd73a Aurélie Siberchicot13 December 2018, 09:31:12 UTCClean R files13 December 2018, 09:31:12 UTC
1516429 Aurélie Siberchicot13 December 2018, 09:18:05 UTCCorrect misprint and add bibliographic reference in DESCRIPTION13 December 2018, 09:18:05 UTC
cbef8d8 Aurélie Siberchicot13 December 2018, 09:16:10 UTCChange 'dontrun' into 'donttest' in the examples13 December 2018, 09:16:10 UTC
365a9bf Marie-laure DELIGNETTE-MULLER13 December 2018, 09:01:10 UTCAdd of a new column in the results (yextrem)13 December 2018, 09:01:10 UTC
4c883b4 Marie-laure DELIGNETTE-MULLER04 December 2018, 10:26:57 UTCremoving of the accent in Aurelie04 December 2018, 10:26:57 UTC
8340826 Marie-laure DELIGNETTE-MULLER04 December 2018, 10:17:18 UTCtestthat only on windows and not on CRAN due to differences of nls results on selected probe line 62 for GP model (AIC.val = 100.32 on Windows and 102.05).04 December 2018, 10:17:18 UTC
845b47b Marie-laure DELIGNETTE-MULLER04 December 2018, 07:53:19 UTCUpdate of the tutorial (for new columns in the results)04 December 2018, 07:53:19 UTC
6ffaf9d Marie-laure DELIGNETTE-MULLER04 December 2018, 07:01:30 UTCMerge branch 'master' of ssh://umr5558-gitlab.univ-lyon1.fr:10022/aursiber/DRomics04 December 2018, 07:01:30 UTC
0fa2bb7 Marie-laure DELIGNETTE-MULLER03 December 2018, 11:00:10 UTCUse by bmdcalc of y0 and xextrem now calculated in drcfit03 December 2018, 11:00:10 UTC
80bec3b Marie-laure DELIGNETTE-MULLER03 December 2018, 10:36:06 UTCAdd of tests with testthat, add of new columns in the dataframe of results (y0, yrange, xextrem) and correction of the trend for Gauss-probit curves with xextrem == 003 December 2018, 10:36:06 UTC
83500b4 Aurélie Siberchicot28 November 2018, 10:51:54 UTCAdd some items on the homepage of the shiny app28 November 2018, 10:51:54 UTC
117950d Aurélie Siberchicot28 November 2018, 10:45:44 UTCAdd the EST citation in the shiny app home page28 November 2018, 10:45:44 UTC
4b67ded Marie-laure DELIGNETTE-MULLER27 November 2018, 15:34:47 UTCAdd of the citation (EST paper), modification of the description file and the news, and of a first test using testthat27 November 2018, 15:34:47 UTC
49bdf4c Aurélie Siberchicot08 November 2018, 14:49:08 UTCUdpate rintall.txt file for the shiny app08 November 2018, 14:49:08 UTC
3479db4 Marie-laure DELIGNETTE-MULLER23 October 2018, 13:06:56 UTCMinor modifications in bmdcalc for a better profiling23 October 2018, 13:06:56 UTC
d5d2064 Aurélie Siberchicot12 October 2018, 10:25:25 UTCOptimize the omicdata function: transpose the data in order to use tapply on columns instead of rows12 October 2018, 10:25:25 UTC
43e4ef0 Aurélie Siberchicot10 October 2018, 15:17:27 UTCUpdate the shiny app (message for users to wait)10 October 2018, 15:17:27 UTC
9b9d012 Aurélie Siberchicot27 September 2018, 13:35:20 UTCUpdate server.R27 September 2018, 13:35:20 UTC
cf87ab4 Aurélie Siberchicot27 September 2018, 08:58:58 UTCUpdate server.R27 September 2018, 08:58:58 UTC
2ccf4f8 Aurélie Siberchicot31 August 2018, 13:14:24 UTCClean and update the format of the imported and exported data31 August 2018, 13:14:24 UTC
72fa17f Marie-laure DELIGNETTE-MULLER30 August 2018, 07:58:11 UTCnew version of the tutorial modified by Floriane30 August 2018, 07:58:11 UTC
9dba966 Aurélie Siberchicot11 July 2018, 14:24:34 UTCUpdate the configuration file of the shiny app11 July 2018, 14:24:34 UTC
0ae3525 Aurélie Siberchicot29 June 2018, 13:21:52 UTCAdd files to configure the shiny app on the shiny server29 June 2018, 13:21:52 UTC
6356fa2 Aurélie Siberchicot18 June 2018, 14:16:55 UTCAdd the DRomics tutorial in the shiny app18 June 2018, 14:16:55 UTC
dceb9e7 Marie-laure DELIGNETTE-MULLER18 June 2018, 14:05:05 UTCFix the BUG in bmdcalc due to NaN counted by is.na() and make the examples shorter to run18 June 2018, 14:05:05 UTC
1428b76 Aurélie Siberchicot18 June 2018, 13:00:43 UTCUpdate the DESCRIPTION file according to CRAN rules18 June 2018, 13:00:43 UTC
f3b5b09 Aurélie Siberchicot14 June 2018, 16:27:00 UTCUpdate the shiny app: the progress bar becomes a message for users14 June 2018, 16:27:00 UTC
51f9dbe Aurélie Siberchicot14 June 2018, 14:09:00 UTCUpdate the shiny app (add a contact in the home panel)14 June 2018, 14:09:00 UTC
8fc4bd4 Marie-laure DELIGNETTE-MULLER13 June 2018, 15:13:12 UTCsupress the limitation of plot.drcfit to max 20 items13 June 2018, 15:13:12 UTC
54c6663 Marie-laure DELIGNETTE-MULLER13 June 2018, 15:09:25 UTCreplacing *omic data by *omics data and supress sensitivity value13 June 2018, 15:09:25 UTC
747295c Aurélie Siberchicot13 June 2018, 14:40:00 UTCcorrect a bug in the shiny app (downloaded file extensions)13 June 2018, 14:40:00 UTC
00298b7 Aurélie Siberchicot13 June 2018, 14:20:31 UTCcorrect a bug in the shiny app (dowload button in the step 3)13 June 2018, 14:20:31 UTC
e7a18c2 Aurélie Siberchicot06 June 2018, 12:50:29 UTCUpdate the shiny app: FDR, z and x are now textInput, no longer numericInput06 June 2018, 12:50:29 UTC
27e0a76 Marie-laure DELIGNETTE-MULLER06 June 2018, 06:10:41 UTCcorrection of bmdcal in bmdcalc in a link06 June 2018, 06:10:41 UTC
5723de8 Marie-laure DELIGNETTE-MULLER06 June 2018, 06:00:54 UTCModification of the introductive text and removing of the metabolomic data set06 June 2018, 06:00:54 UTC
7d00658 Marie-laure DELIGNETTE-MULLER05 June 2018, 13:08:45 UTCIncluding recommendations in some help buttons05 June 2018, 13:08:45 UTC
cef410c Aurélie Siberchicot04 June 2018, 16:19:31 UTCUpdate the step 4 fo the shiny app to print only 4 significant digits04 June 2018, 16:19:31 UTC
03e5cd5 Aurélie Siberchicot04 June 2018, 16:18:31 UTCUpdate the main page of the shiny app04 June 2018, 16:18:31 UTC
a51cd6d Aurélie Siberchicot04 June 2018, 16:15:57 UTCadd logos for shiny app04 June 2018, 16:15:57 UTC
a95b51a Marie-laure DELIGNETTE-MULLER29 May 2018, 09:48:00 UTCnew general .Rd for DRomics29 May 2018, 09:48:00 UTC
fac204b Marie-laure DELIGNETTE-MULLER29 May 2018, 08:43:38 UTCminor correction in the extended description29 May 2018, 08:43:38 UTC
4baa21b Marie-laure DELIGNETTE-MULLER29 May 2018, 08:17:56 UTCWriting of an extended version or the description of the package29 May 2018, 08:17:56 UTC
f906147 Marie-laure DELIGNETTE-MULLER29 May 2018, 07:02:53 UTCstandardisation of the writing of BMD-zSD and BMD-xfold in the text parts29 May 2018, 07:02:53 UTC
3a629c6 Aurélie Siberchicot25 May 2018, 14:55:42 UTCUpdate interface in the shiny app25 May 2018, 14:55:42 UTC