1. Rtpca
  2. Graph
Graph of Rtpca
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  • c1922eb (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 11:20:19 -0400;
  • 742b5bf (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 11:20:19 -0400;
  • 265cebe bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:22:21 -0400;
  • 32664ea (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:22:21 -0400;
  • 2356eb9 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2022-06-10 10:17:41 +0200;
  • 3d3c267 changed email address by Nils Kurzawa <nils.kurzawa@embl.de> 2022-05-03 15:19:47 +0200;
  • 74d56ce bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 16:06:23 +0000;
  • 8f5d600 (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 16:06:23 +0000;
  • 2714b9f bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 17:00:47 +0000;
  • 5502202 (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 17:00:47 +0000;
  • b7e2b86 bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:53:36 +0000;
  • acf0a22 (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:53:36 +0000;
  • 75715de Merge branch 'master' of https://github.com/nkurzaw/Rtpca by Nils Kurzawa <nils.kurzawa@embl.de> 2021-04-21 14:10:38 +0200;
  • 799b184 added rmarkdown to suggested package list by Nils Kurzawa <nils.kurzawa@embl.de> 2021-04-21 14:10:28 +0200;
  • e5d7b84 Update .travis.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-12-01 10:07:39 +0100;
  • bb71e4d fixed typo in complex tpca function message by Nils Kurzawa <nils.kurzawa@embl.de> 2020-11-27 14:42:41 +0100;
  • d2ad09d incoporated feedback from codereview - significant speed up of all major functions by Nils Kurzawa <nils.kurzawa@embl.de> 2020-11-27 14:22:28 +0100;
  • b707a85 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2020-10-29 10:11:27 +0100;
  • f4978ea Merge remote-tracking branch 'upstream/master' by Nils Kurzawa <nils.kurzawa@embl.de> 2020-10-29 10:10:22 +0100;
  • 9724a06 known TP interactions are now removed from randomly generated ones by Nils Kurzawa <nils.kurzawa@embl.de> 2020-10-29 10:06:04 +0100;
  • bd61acd fixed typo in vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-10-29 10:04:46 +0100;
  • 0b1aea9 bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:58:32 -0400;
  • cc51235 (origin/RELEASE_3_12, RELEASE_3_12) bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:58:32 -0400;
  • d9fa996 added citation to vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-08-30 16:52:53 +0200;
  • 981e288 fixed bug which included x:x pairs in PPI ROC analysis by Nils Kurzawa <nils.kurzawa@embl.de> 2020-08-30 16:48:20 +0200;
  • 2a09da2 fixed typos in string_ppi_df description by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-29 08:39:23 +0200;
  • ee689ca added package citation file by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-28 17:38:27 +0200;
  • ed3248a made PPiRocTable generating function more efficient by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-14 10:53:38 +0200;
  • 01702d6 updated manual for plotComplexRoc by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-14 10:52:38 +0200;
  • 8d2252c fixed typo in vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-22 16:15:37 +0200;
  • eb5ddf6 added sentence to vignette clarifying the origin of the string db data frame by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-22 15:07:45 +0200;
  • 8822532 adressed remaining required review comments by adding more accessory functions by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-18 10:39:42 +0200;
  • 4ab653f added more structure and explanations to vignette, reduced long code lines, created accessor method for tpcaResult object, to do: more accessor methods by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-11 11:43:54 +0200;
  • 0057fbe adressed first rounds of comments, still some left by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-09 16:59:44 +0200;
  • 21bf319 extended package description (BiocCheck), added NEWS file, completeed return manual of tpcaResult class by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 16:49:33 +0200;
  • 59150af addressed 'incomplete final line found' in two test files, version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 16:26:03 +0200;
  • 53819c0 added Rmd file to create github README file by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 15:27:29 +0200;
  • a17d029 Update README.md by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-05 13:44:04 +0200;
  • 5728dcf updated README.md by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 13:37:22 +0200;
  • 1138712 updated README.md by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 13:33:52 +0200;
  • b4d97d5 updated R version dependency and corrected set package version to comply with Bioc submission by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 12:47:03 +0200;
  • b916b25 updated namespace to export generic functions by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 12:46:17 +0200;
  • b65db8d exchanged usage of @ access result table by new generic function in vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 12:45:43 +0200;
  • 531afd5 added .gitignore and .Rbuilignore by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 12:44:02 +0200;
  • d3ee3d4 added generic getter functions to retrieve result tables by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 12:43:31 +0200;
  • 06f01d4 Update README.md by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-05 08:51:19 +0200;
  • ce5af11 resolved remaining 'no visibile binding for global variable' issues by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-05 08:47:39 +0200;
  • aa58d34 addressed more Rcheck notes by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-02 12:27:43 +0200;
  • 03f510b removed commented code from earlier hdf5 matrix utlization, updated roxygen version, adressed some 'non-visible binding' notes by Nils Kurzawa <nils.kurzawa@embl.de> 2020-05-29 18:15:20 +0200;
  • e47c06a fixed bug introduced by previous commit by Nils Kurzawa <nils.kurzawa@embl.de> 2020-05-28 17:49:39 +0200;
  • 6884f56 replaced sapplys with vapplys by Nils Kurzawa <nils.kurzawa@embl.de> 2020-05-28 16:48:14 +0200;
  • e5e09cf fixed bug so that plotPPIProfile now has numeric temperature on x-axis instead of chracter by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-15 11:39:10 +0200;
  • a8a704b Update Rtpca.Rmd by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-04-08 06:21:33 +0200;
  • 8c23a8d updated plotPPiProfiles function to include spline fit and niver colors by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-07 17:07:19 +0200;
  • e49ee7a fixed wrong issue of Tan et al. reference by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-07 16:32:08 +0200;
  • 55a054b updated vignette and README by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-07 16:29:23 +0200;
  • 1f46d7c updated vignette to include ctrl and contrast name usage by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-07 14:24:58 +0200;
  • de254a7 updated supplied dataset of PPI interactions within complex to include only stringDB interactions by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-07 14:24:19 +0200;
  • f6f9bdc updated references for vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-26 11:23:59 +0100;
  • 17df522 extended vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-25 19:25:54 +0100;
  • 7ebe360 fixed plot label annotation bug by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-25 19:25:24 +0100;
  • 0d2464d resolved fdrtool import warning, added documentation for additional parameter complexAnno for runDiffTPCA by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-25 16:18:32 +0100;
  • 6886817 added possibility to use BH and fdrtool by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-25 14:34:45 +0100;
  • e3bd0ae added possibility to use fdrtool for local fdr estimation by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-25 14:33:12 +0100;
  • a299f33 updated filterDistMat to speed it up by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-24 19:48:35 +0100;
  • b5fa523 updated plotPPiProfiles function documentation by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-24 16:30:15 +0100;
  • d5ccf36 plotPPiProfiles is now exported and documented by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-24 16:01:00 +0100;
  • 8ed4225 fixed plotPPiProfile test by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-24 13:22:27 +0100;
  • 0e71e30 extedended plotPPiProfile function to matrices, added test for function by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-24 12:47:30 +0100;
  • c3d6d75 started with function for plotting melting curves of protein pairs across conditions by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-23 18:19:28 +0100;
  • 647f220 added possibility to supply condition names which are incorporated into figures etc. by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-23 16:24:13 +0100;
  • 8cade19 fixed plot label error by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-21 15:25:11 +0100;
  • 51221aa fixed diffTpca volcano plot by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-21 14:13:42 +0100;
  • 4eed442 adapted test to bug fix in F statistic computation by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-21 13:50:11 +0100;
  • 78f4793 changed usage of summary method and set 0 pvalues to lowet machine value by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-21 13:44:10 +0100;
  • ec4172f fixed error in computing RSS by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-20 16:15:29 +0100;
  • 4ddb8c7 fixed typo in runDiffTpca function messages by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-19 17:30:37 +0100;
  • 5392f6b updated string dataset by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-19 17:04:34 +0100;
  • 3b3944b Update README.md by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-03-19 10:51:22 +0100;
  • 0d7af01 updated README by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-19 10:50:15 +0100;
  • a0c0536 updated vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-19 10:43:32 +0100;
  • 3f6b417 fixed bug in function that lead to NAs in euclidean distance being evaluated and add data.R file by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-19 10:42:16 +0100;
  • ea4c704 added usage section to datasets by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-18 20:18:53 +0100;
  • ad83035 added vignette and ppi/complex annotation dataset by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-18 15:59:24 +0100;
  • ffc7c4b fixed typo in message for runTPCA function and added messages for runDiffTpca function by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-18 08:21:33 +0100;
  • 5dab5fd reduced transperancy of non-hit dots in volcano plots by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-12 17:20:54 +0100;
  • 46d27c2 added TPCA test for ppis using same function as for complexes by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-12 14:20:26 +0100;
  • 94780bd fixed bug in complexRocAnalysis function and fixed some typos by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-11 16:48:52 +0100;
  • 81bdac4 added function for perfoming ROC analysis based on protein complexes by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-11 16:32:19 +0100;
  • 3886b59 added complexRocTable slot to tpcaResult class by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-11 15:38:53 +0100;
  • cc16f16 added tests for tpca volcano plots by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-10 17:34:04 +0100;
  • 75f979c added missing manual for plotTpcaVolcano by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-10 17:06:53 +0100;
  • b074623 finalized classical tpca analysis and harmonized plotting functions by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-10 16:43:28 +0100;
  • 62b813e added slot for output table of non-differential tpca analysis and adjusted show function by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-10 16:42:17 +0100;
  • be14ba3 added missing manual files for volcanoPlot function and tpcaResult class by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-09 12:16:13 +0100;
  • 22d3601 added tpca result slot to tpcaResult object by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-09 11:35:22 +0100;
  • b080f6a added missing manual files by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-06 16:48:21 +0100;
  • 8f5edd3 runDiffTPCA and plotDiffTpcaVolcano are now exported by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-06 16:47:30 +0100;
  • 7e652f9 added test for runDiffTPCA functions, more to come by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-06 16:25:43 +0100;
  • 9ad0185 modified filterDistMat function to circumvent problems resulting von R's matrix to vector conversion by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-06 16:24:56 +0100;