Graph ofTPP2D
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  • 8b5ab49 (HEAD -> master, origin/master, origin/HEAD) added new function for faster fstat null distribution estimation and bumped version by Nils Kurzawa <nils.kurzawa@embl.de> 2022-11-24 14:09:07 +0100;
  • e933a98 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2022-11-17 09:37:07 +0100;
  • 999a000 fixed hyphens by Nils Kurzawa <nils.kurzawa@embl.de> 2022-11-17 09:36:07 +0100;
  • d600692 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 11:19:54 -0400;
  • ba3a310 (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 11:19:54 -0400;
  • f4fc4db added a filtering step in data import to prevent NA entries by Nils Kurzawa <nils.kurzawa@embl.de> 2022-06-29 16:30:43 +0200;
  • d09df2c Merge branch 'master' of https://github.com/nkurzaw/TPP2D by Nils Kurzawa <nils.kurzawa@embl.de> 2022-06-10 10:14:39 +0200;
  • 37fb1c1 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2022-06-10 10:14:33 +0200;
  • 4db0b44 Update r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2022-05-03 15:40:25 +0200;
  • 446e1c3 Update and rename r2.yml to r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2022-05-03 15:31:01 +0200;
  • 37e6657 Update README.md by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2022-05-03 15:25:41 +0200;
  • aae6101 Delete r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2022-05-03 15:24:42 +0200;
  • c770b5c Create r2.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2022-05-03 15:24:26 +0200;
  • 414a52c changed email address by Nils Kurzawa <nils.kurzawa@embl.de> 2022-05-03 15:20:38 +0200;
  • 1223252 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 15:55:55 +0000;
  • 80a0003 (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 15:55:55 +0000;
  • 0fdc970 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 16:51:59 +0000;
  • 2456623 (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 16:51:59 +0000;
  • 2bd83c1 fixed warning induced by difference between man and roxygen code in plot2dTppFit function by Nils Kurzawa <nils.kurzawa@embl.de> 2021-05-25 15:04:27 +0200;
  • 846bcc0 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 16:43:43 +0000;
  • 432c4fa (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 16:43:43 +0000;
  • 8503351 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2021-04-21 14:07:37 +0200;
  • 7169732 added rmarkdown as suggested package by Nils Kurzawa <nils.kurzawa@embl.de> 2021-04-21 14:05:26 +0200;
  • 20dcf00 Merge branch 'master' of https://github.com/nkurzaw/TPP2D by Nils Kurzawa <nils.kurzawa@embl.de> 2021-02-08 17:03:19 +0100;
  • 2ce2bd0 minor changes to default plotting settings for plot2DTPPFit by Nils Kurzawa <nils.kurzawa@embl.de> 2021-02-08 17:03:11 +0100;
  • 2d8c249 Update .travis.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-30 19:27:44 +0100;
  • de8c424 Merge branch 'master' of https://github.com/nkurzaw/TPP2D by Nils Kurzawa <nils.kurzawa@embl.de> 2020-11-30 19:22:44 +0100;
  • 3cbf1cd updated reference in vignette and optimized plots of fits by Nils Kurzawa <nils.kurzawa@embl.de> 2020-11-30 19:22:36 +0100;
  • 7095212 Update r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-30 18:22:48 +0100;
  • 0398862 Update r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-30 18:12:23 +0100;
  • dd216d6 added more option to plot function for TPP2D fit by Nils Kurzawa <nils.kurzawa@embl.de> 2020-11-30 17:56:08 +0100;
  • a8d1fed updated reference by Nils Kurzawa <nils.kurzawa@embl.de> 2020-11-13 16:15:20 +0100;
  • 1ed7160 Merge remote-tracking branch 'upstream/master' by Nils Kurzawa <nils.kurzawa@embl.de> 2020-11-13 16:09:14 +0100;
  • 66a6e61 Update r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-12 17:47:28 +0100;
  • abb18f9 Update r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-12 17:46:03 +0100;
  • 88e32d2 Update r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-12 16:54:26 +0100;
  • 22c9a48 Update .gitignore by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-12 16:51:29 +0100;
  • 260e8f9 Create r.yml by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-11-12 16:50:55 +0100;
  • 17f3e9e 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 11:46:04 -0400;
  • b5b80d6 (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 11:46:04 -0400;
  • e4dec7b corrected F stat shrinkage by Nils Kurzawa <nils.kurzawa@embl.de> 2020-09-28 10:10:51 +0200;
  • 0ccc97b readded install instruction for BiocManager devel version by Nils Kurzawa <nils.kurzawa@embl.de> 2020-08-28 15:17:11 +0200;
  • 617e7fe Update .travis.yml to see if this can fix travis CI problem installing BiocManager by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-08-28 11:15:14 +0200;
  • 5a6cf13 updated .checkRatioRef function to omit use of by Nils Kurzawa <nils.kurzawa@embl.de> 2020-08-28 11:02:47 +0200;
  • 776fc19 fixed typo in check config table function by Nils Kurzawa <nils.kurzawa@embl.de> 2020-08-28 10:08:16 +0200;
  • ef92dbd updated function to compute p-values and to visualize volcano plot by Nils Kurzawa <nils.kurzawa@embl.de> 2020-08-26 09:26:39 +0200;
  • ce853b8 incorporated feedback from code-review into fdr functions by Nils Kurzawa <nils.kurzawa@embl.de> 2020-08-04 18:16:06 +0200;
  • ab50974 Update fdr_funcs.R by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-08-04 16:58:51 +0200;
  • 7b44e94 version bumbp by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-13 13:29:18 +0200;
  • e7ea5f2 updated reference in vignette, prevent code for showing overview figure from echoing by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-13 13:28:57 +0200;
  • 1c6e0f8 version bump tp 1.5.7 by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-08 08:14:21 +0200;
  • 59ab700 updated fcHeatmap plotting function to also work for destabilization by Nils Kurzawa <nils.kurzawa@embl.de> 2020-07-08 08:13:49 +0200;
  • 0885df8 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 by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-22 11:38:06 +0200;
  • a462a04 Update NEWS by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-20 17:30:04 +0200;
  • 4b0819b Update NEWS by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-20 17:27:57 +0200;
  • 58a718f (origin/RELEASE_3_11, RELEASE_3_11) bug fix: moderated F-statistic uses now also moderated degrees of freedom df2 by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-20 17:06:20 +0200;
  • 69c7ac4 decided to not prevent NAs for FDR estimation if denominator of pi == 0 by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-20 17:02:32 +0200;
  • 29ad5b2 revised vignette, version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-20 16:46:45 +0200;
  • 5db33b3 optimized heatmap function parameter usage by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-20 08:35:02 +0200;
  • a80d4f9 Merge branch 'master' of https://github.com/nkurzaw/TPP2D by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-19 17:49:33 +0200;
  • 3fab3a9 added volcano plot function, small fix in FDR function, extended vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-19 17:49:26 +0200;
  • 1ff7560 Update README.md by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-19 15:44:41 +0200;
  • 4a3478a modified resolveAmbiguousProteinNames to force gene name-centered analysis by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-19 14:42:15 +0200;
  • 9099623 added ggtitle to fcHeatmap by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-18 14:59:40 +0200;
  • f39665a now also added actual code of plot2dTppFcHeatmap by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-17 17:24:34 +0200;
  • 7115034 added plotting function for heatmap visualization by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-17 16:59:50 +0200;
  • 385f4c3 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-16 18:55:10 +0200;
  • c1b098a Update NEWS by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-16 16:34:32 +0200;
  • 267059f Update NEWS by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-16 16:33:42 +0200;
  • 14cc378 finalized defuncing computeFdr by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-16 16:32:29 +0200;
  • bb6b9a6 removed R/TPP2D-deprecated.R by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-16 15:57:15 +0200;
  • 3aafdcf defunct computeFdr by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-16 15:56:23 +0200;
  • 391b90f Update NEWS by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-16 15:27:23 +0200;
  • d3d20d1 updated vignette, updated roxygen version by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-16 15:25:00 +0200;
  • 2a94127 Update README.md by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-16 15:21:36 +0200;
  • e6bbf9e re-added travis file by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-16 15:14:00 +0200;
  • 1fc975b Update README.md by nkurzaw <32863918+nkurzaw@users.noreply.github.com> 2020-06-16 15:08:05 +0200;
  • 693355c incorporated comment by Constantin by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-08 16:28:32 +0200;
  • 3dccf89 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2020-06-01 11:06:13 +0200;
  • 00d53b6 added citation file by Nils Kurzawa <nils.kurzawa@embl.de> 2020-05-12 14:18:07 +0200;
  • 8ba895e Merge remote-tracking branch 'upstream/master' by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-28 08:02:18 +0200;
  • b3eb139 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 19:27:04 +0000;
  • 86e42c9 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 19:27:04 +0000;
  • bab0266 updated README by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-20 10:34:19 +0200;
  • ec90d81 version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-17 11:21:04 +0200;
  • a454a00 updated news by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-17 11:20:40 +0200;
  • ed03515 bumped version by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-09 15:52:20 +0200;
  • e06805a added option to squeezeVariance also for getPvalues function by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-09 15:48:44 +0200;
  • 045c02d added option to shrink F stat denominator using limma::squeezeVar by Nils Kurzawa <nils.kurzawa@embl.de> 2020-04-09 10:24:10 +0200;
  • 3f0cb5e added function to compute pEC50 at specified temperature for protein of interest by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-30 17:32:18 +0200;
  • 73aa36c updated DESCRIPTION to include method name DLPTP by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-28 11:11:55 +0100;
  • 14516f4 bumped package version by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-26 12:18:10 +0100;
  • dc37f1f improved getFDR and findHits behavior in dealing with NA F statistics by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-26 12:17:24 +0100;
  • 215eb9d prevented NA F statistics from being considered for FDR estimation by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-19 16:29:04 +0100;
  • a0a63b4 updated bib file for vignette by Nils Kurzawa <nils.kurzawa@embl.de> 2020-03-18 11:23:10 +0100;
  • 9466047 replaced function for computing p-values, bumped version to trigger bioc build by Nils Kurzawa <nils.kurzawa@embl.de> 2020-01-29 10:22:42 +0100;
  • 08e4232 replaced function for computing p-values by Nils Kurzawa <nils.kurzawa@embl.de> 2020-01-29 10:21:15 +0100;
  • ced496d added new function for computing p-values to replace kernel density-based one, added missing documentation for gg_qq plot parameter by Nils Kurzawa <nils.kurzawa@embl.de> 2020-01-29 10:03:26 +0100;
  • f4b2dfe added parameter to make indentity line in qq plots optional by Nils Kurzawa <nils.kurzawa@embl.de> 2020-01-28 13:12:21 +0100;
  • 099bcae version bump by Nils Kurzawa <nils.kurzawa@embl.de> 2020-01-26 15:38:04 +0100;