Bioconductor Code: INSPEcT

Graph of INSPEcT

fc7e610 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 10:44:09 -0400;
651996a (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 10:44:09 -0400;
81e6936 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 10:40:18 -0400;
d98fcb7 (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 10:40:18 -0400;
5409025 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 11:11:51 -0400;
aff3971 (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 11:11:51 -0400;
3078861 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 15:26:03 +0000;
8ba12ec (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 15:26:03 +0000;
e99d196 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 16:21:19 +0000;
ed551fb (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 16:21:19 +0000;
405e197 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 16:14:25 +0000;
b877791 (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 16:14:25 +0000;
9c876c8 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 11:06:18 -0400;
d952c98 (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 11:06:18 -0400;
07cd1ed (origin/RELEASE_3_11, RELEASE_3_11) version bump to 1.18.1 by ste-depo <ste.depo@gmail.com> 2020-10-05 14:08:00 +0200;
d1e0414 merged version number to 1.19.1 by ste-depo <ste.depo@gmail.com> 2020-09-28 16:08:18 +0200;
233f3c8 removed the check of INSPEcT version from steady-state method compareSteadyNoNascent by ste-depo <ste.depo@gmail.com> 2020-09-28 16:03:38 +0200;
08fdad7 added citations by ste-depo <ste.depo@gmail.com> 2020-09-28 13:48:00 +0200;
cfa9bd7 merge with upstream/RELEASE_3_11 by ste-depo <ste.depo@gmail.com> 2020-09-28 13:44:30 +0200;
206958c added new citations by ste-depo <ste.depo@gmail.com> 2020-09-28 13:13:15 +0200;
5c2a7a0 fixed controls of INSPEcT object version by ste-depo <ste.depo@gmail.com> 2020-09-02 17:40:50 +0200;
5463084 added the possibility to model intronless genes for derivative modeling; improved the plotGene function by ste-depo <ste.depo@gmail.com> 2020-09-02 17:15:04 +0200;
b8c1214 documentation updated by ste-depo <ste.depo@gmail.com> 2020-08-28 16:09:49 +0200;
4831df1 fixed bugs in compareSteady method by ste-depo <ste.depo@gmail.com> 2020-08-28 15:25:55 +0200;
a1b6264 fixed bugs in compareSteady method by ste-depo <ste.depo@gmail.com> 2020-08-28 15:20:55 +0200;
ca1a7ed version bump to 1.19.1 by ste-depo <ste.depo@gmail.com> 2020-08-09 10:30:02 +0200;
6b058f5 Merge branch 'master' of github.com:ste-depo/INSPEcT by ste-depo <ste.depo@gmail.com> 2020-08-09 10:27:10 +0200;
021682f steady-state methods: fixed a bug with unresolved genes by ste-depo <ste.depo@gmail.com> 2020-08-09 10:26:34 +0200;
a113549 Merge pull request <a href="#30">#30</a> from mfurla/master by Stefano de Pretis <ste.depo@gmail.com> 2020-08-09 10:13:41 +0200;
9ab3e23 removed prova_fast.sh by De Pretis Stefano <ste.depo@gmail.com> 2020-08-09 10:12:00 +0200;
e1cb553 automatic version numbering in INSPEcT object by De Pretis Stefano <ste.depo@gmail.com> 2020-08-09 10:08:40 +0200;
4fc9979 Merge pull request <a href="#29">#29</a> from mfurla/master by Stefano de Pretis <ste.depo@gmail.com> 2020-08-09 09:26:09 +0200;
c43db1e merge between mfurla and ste-depo changes by De Pretis Stefano <ste.depo@gmail.com> 2020-06-05 11:19:14 +0200;
df5f876 INSPEcT_steadyNoNascent referenceCondition slot set to character to fix a bug that occurred when no reference was set in the analysis by De Pretis Stefano <ste.depo@gmail.com> 2020-06-05 11:10:27 +0200;
50401ce Removal of the constrain on time series design. by mfurla <mattia.furlan776@edu.unito.it> 2020-06-04 12:04:00 +0200;
1c8f951 Flag in newINSPEcT to decide if not finite rates first guess should be imputed or not by mfurla <mattia.furlan776@edu.unito.it> 2020-06-03 10:02:29 +0200;
540b166 Custom threshold for gene filter in newINSPEcT function, avoid null entries in steady state no nascent null model inference by Mattia Furlan <mattia@Mattias-MacBook-Pro.local> 2020-06-01 16:17:01 +0200;
421f5ce Merge pull request <a href="#27">#27</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-05-08 15:55:39 +0200;
b35e7dc fixed a bug in newINSPEcT genes filtering, removed non-useful warnings thrown by newINSPEcT in the NoNascent mode by De Pretis Stefano <ste.depo@gmail.com> 2020-05-08 15:52:59 +0200;
da3017d 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 18:49:55 +0000;
caa2883 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 18:49:55 +0000;
0242ec0 Merge pull request <a href="#25">#25</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-04-15 16:24:56 +0200;
192aee7 1.17.15 - updated documentation following 1.17.14 modifications by De Pretis Stefano <ste.depo@gmail.com> 2020-04-15 16:23:04 +0200;
7dad95f Merge pull request <a href="#24">#24</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-04-13 11:31:03 +0200;
19d5304 1.17.14 - serial parallelization (i.e. no parallelization) by default in all methods by De Pretis Stefano <ste.depo@gmail.com> 2020-04-13 11:29:33 +0200;
cdb003c Merge pull request <a href="#23">#23</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-04-08 17:16:50 +0200;
5326f09 version 1.17.13 - added modeling and fit output to PDF and TSV output of the GUI - dependency to R >= 3.6 - removed table(geneClass()) from evaluation of vignette INSPEcT in the hope that will solve the TIMEOUT on Windows BioC server by De Pretis Stefano <ste.depo@gmail.com> 2020-04-08 16:34:56 +0200;
1eb837a Merge pull request <a href="#22">#22</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-02-24 11:11:27 +0100;
6c9f278 vignette and documentation bug-fixing relative to version 1.17.11 by De Pretis Stefano <ste.depo@gmail.com> 2020-02-24 11:10:04 +0100;
3ceed78 Merge pull request <a href="#21">#21</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-02-21 22:45:12 +0100;
b89af4c added INSPEcT_steadyNoNascent class and methods by De Pretis Stefano <ste.depo@gmail.com> 2020-02-21 22:40:38 +0100;
cf63af0 Merge branch 'master' of https://github.com/mfurla/INSPEcT by De Pretis Stefano <ste.depo@gmail.com> 2020-02-19 14:44:55 +0100;
988b7bc version 1.17.10 added functionalities to quantify expressions from BigWig files and without replicates (checks for replicates needs to be added within newINSPEcT) by De Pretis Stefano <ste.depo@gmail.com> 2020-02-19 14:40:40 +0100;
57a0ad7 (origin/RELEASE_3_10, RELEASE_3_10) version bump to 1.16.3 by ste-depo <ste.depo@gmail.com> 2020-02-03 15:42:10 +0100;
2fc5325 Merge pull request <a href="#20">#20</a> from ste-depo/master by ste-depo <ste.depo@gmail.com> 2020-02-03 15:41:31 +0100;
0355667 Merge pull request <a href="#19">#19</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-02-03 15:36:54 +0100;
c02e1ea Merge branch 'master' into master by ste-depo <ste.depo@gmail.com> 2020-02-03 15:36:45 +0100;
16a76f4 version bump to 1.17.9 by De Pretis Stefano <ste.depo@gmail.com> 2020-02-03 15:31:21 +0100;
581950d - INSPEcT_GUI user-defined mode back with smooth visualization of functional forms - examples beta pars modified to 1 in the vignette by De Pretis Stefano <ste.depo@gmail.com> 2020-02-03 15:25:22 +0100;
8fc19b9 Merge pull request <a href="#18">#18</a> from ste-depo/master by ste-depo <ste.depo@gmail.com> 2020-01-10 14:17:34 +0100;
afa71c8 Merge branch 'RELEASE_3_10' into master by ste-depo <ste.depo@gmail.com> 2020-01-10 14:17:25 +0100;
49df19f Merge pull request <a href="#17">#17</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-01-07 16:14:52 +0100;
9c17165 added out.width argument to INSPEcT_GUI vignette figure chunks by De Pretis Stefano <ste.depo@gmail.com> 2020-01-07 16:13:43 +0100;
26c31f0 Merge pull request <a href="#16">#16</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2020-01-05 11:31:52 +0100;
b5b3872 adapted dpi argument of include_graphics function in INSPEcT_GUI vignette by De Pretis Stefano <ste.depo@gmail.com> 2020-01-05 11:30:24 +0100;
2245595 Merge pull request <a href="#15">#15</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2019-12-26 17:22:39 +0100;
c295420 forced dpi to 120 for imported images in INSPEcT_GUI vignette by De Pretis Stefano <ste.depo@gmail.com> 2019-12-26 17:19:25 +0100;
e7bed9e Merge pull request <a href="#14">#14</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2019-12-16 16:16:55 +0100;
6fbbd5e the simulated datasets were created with R 3.6.1 by De Pretis Stefano <ste.depo@gmail.com> 2019-12-16 16:13:44 +0100;
cb44f81 bump to 1.16.1 by ste-depo <ste.depo@gmail.com> 2019-12-13 12:25:00 +0100;
13f91e2 bug fix in featureNames setReplaceMethod by De Pretis Stefano <ste.depo@gmail.com> 2019-12-12 10:54:02 +0100;
d83e1c4 Merge pull request <a href="#13">#13</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2019-12-11 16:41:18 +0100;
4d4b175 updated minimization_status.png by De Pretis Stefano <ste.depo@gmail.com> 2019-12-11 16:31:02 +0100;
efc5f8e updated INSPEcT-GUI vignette; version bump to 1.17.4 by De Pretis Stefano <ste.depo@gmail.com> 2019-12-11 16:30:30 +0100;
b25de98 Merge pull request <a href="#12">#12</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2019-12-06 16:50:00 +0100;
609f35c yet another bug fix for INSPEcT-GUI by De Pretis Stefano <ste.depo@gmail.com> 2019-12-06 16:13:43 +0100;
e5cc9d2 minor updates to INSPEcT-GUI by De Pretis Stefano <ste.depo@gmail.com> 2019-12-06 14:19:00 +0100;
c16e060 change in the order of items of the left panel of INSPEcR-GUI UI by De Pretis Stefano <ste.depo@gmail.com> 2019-12-06 09:42:21 +0100;
b2fb2fe merged DESCRIPTION by De Pretis Stefano <ste.depo@gmail.com> 2019-12-05 16:30:27 +0100;
ea313c5 modified INSPEcTGUI layout, added M.F. as maintainer and bugfixing in INSPEcTGUI by De Pretis Stefano <ste.depo@gmail.com> 2019-12-05 16:26:31 +0100;
1c436b3 Merge pull request <a href="#11">#11</a> from mfurla/master by ste-depo <ste.depo@gmail.com> 2019-12-05 11:55:52 +0100;
b2b78b7 Merge branch 'master' into master by ste-depo <ste.depo@gmail.com> 2019-12-05 11:55:43 +0100;
bc8b025 added wrap-up functions and fixed code to allow single gene analysis by De Pretis Stefano <ste.depo@gmail.com> 2019-12-05 11:51:06 +0100;
69056c9 Merge remote-tracking branch 'upstream/master' by ste-depo <ste.depo@gmail.com> 2019-11-25 13:23:20 +0100;
183caeb Merge pull request <a href="#10">#10</a> from ste-depo/pr/9 by ste-depo <ste.depo@gmail.com> 2019-11-25 12:18:50 +0100;
5754816 removed unneeded data files by ste-depo <ste.depo@gmail.com> 2019-11-25 12:16:14 +0100;
a5e5db9 updated documentation and datasets by De Pretis Stefano <ste.depo@gmail.com> 2019-11-14 17:30:24 +0100;
7d3b82e changes in class nomenclature and model params accession, removal of unused code - class names follow now the nomenclature from synthesis ('s'), processing ('p') and degradation ('d') - modeling parameters are set via modelRates and only accessed via modelingParams - model selection parameters are set via calculatePvals and only accessed via modeingParams - ratePvals only access to the slot ratePvlas, which is filled by calculateRatePvals by De Pretis Stefano <ste.depo@gmail.com> 2019-11-14 17:02:03 +0100;
8bc268e converted gene class names and simplified geneClass method code by De Pretis Stefano <ste.depo@gmail.com> 2019-11-08 18:07:33 +0100;
fef41e0 ratePvals additional modifications - subset of ratePvals slot in the Extract - removed the argument singleGeneClass from the method 'computeConfidenceIntervals' by De Pretis Stefano <ste.depo@gmail.com> 2019-11-08 10:14:34 +0100;
8e77c6c Updated INSPEcT datasets with the ratePvals slot by De Pretis Stefano <ste.depo@gmail.com> 2019-11-08 09:25:09 +0100;
6653a0d ratePvals modified - calculated at the time of modeling (calculateRatePvals method) - stored into slot ratePvals of the class INSPEcT - p-values adjustment also when they are computed via confidence intervals (nascent and N.F.) by De Pretis Stefano <ste.depo@gmail.com> 2019-11-07 16:29:01 +0100;
79d2cb3 corrected '[' method to subset confidence intervals by De Pretis Stefano <ste.depo@gmail.com> 2019-11-07 10:04:46 +0100;
1df5af5 Suppress warning when plotting to PDF by De Pretis Stefano <ste.depo@gmail.com> 2019-11-06 17:29:59 +0100;
73a7785 Added Fix-Y-Axis & pvals in Y-labels by De Pretis Stefano <ste.depo@gmail.com> 2019-11-06 17:27:33 +0100;
b3db082 Added the slot 'version' to class INSPEcT and the controls to check the version in methods and GUI by De Pretis Stefano <ste.depo@gmail.com> 2019-11-06 13:47:45 +0100;
a7e7b03 Confidence intervals controlled by a button rather than the checkbox by De Pretis Stefano <ste.depo@gmail.com> 2019-11-05 16:12:25 +0100;
2643341 version bumping to 1.17.1 by De Pretis Stefano <ste.depo@gmail.com> 2019-11-05 11:19:51 +0100;
4ab6283 added relative expression checkbox by De Pretis Stefano <ste.depo@gmail.com> 2019-11-05 11:18:41 +0100;
85e1210 bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:39:37 -0400;