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  • 8c60dba (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 11:11:13 -0400;
  • 8ce711f (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2024-10-29 11:11:13 -0400;
  • 88dde65 bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 11:42:19 -0400;
  • 35e881e (origin/RELEASE_3_19, RELEASE_3_19) bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <jwokaty@users.noreply.github.com> 2024-04-30 11:42:18 -0400;
  • 173a2b4 (origin/RELEASE_3_18, RELEASE_3_18) Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 22:39:10 +0100;
  • dfd5166 Updated GHA workflow and simplified pkgdown configs by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 22:37:55 +0100;
  • bf8eb30 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 22:38:21 +0100;
  • d9608e3 Updated GHA workflow and simplified pkgdown configs by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 22:37:55 +0100;
  • 094b642 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 16:22:12 +0100;
  • 44e9ef2 Fixed unit test and added CITATION file by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 16:19:48 +0100;
  • 67fab65 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 16:20:25 +0100;
  • 54569f7 Fixed unit test and added CITATION file by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2024-01-12 16:19:48 +0100;
  • 693339b 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 11:41:44 -0400;
  • c152c0a 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 11:41:44 -0400;
  • 23da58a (origin/RELEASE_3_17, RELEASE_3_17) Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-10-07 20:06:26 +0200;
  • 5415529 Added the option to return dispersal and corrected orthogroup scores as separate variables in calculate_H() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-10-07 20:04:19 +0200;
  • 2b29723 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-10-07 20:04:59 +0200;
  • e9a3ad5 Added the option to return dispersal and corrected orthogroup scores as separate variables in calculate_H() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-10-07 20:04:19 +0200;
  • ffae8b0 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 11:37:54 -0400;
  • 01cccb5 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 11:37:54 -0400;
  • 32e6bdb (origin/RELEASE_3_16, RELEASE_3_16) Bioconductor branch rename from master to devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-03-14 12:49:09 +0100;
  • 8fb5a0e Bioconductor branch rename from master to devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-03-14 12:49:09 +0100;
  • b3a2e59 Fixed bug in GHA workflow by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-24 08:53:20 +0100;
  • 62198c7 Fixed bug in GHA workflow by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-24 08:53:20 +0100;
  • 24ab224 Version bump in release: 1.2.1 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-23 21:31:01 +0100;
  • ff46d01 Updated NEWS file by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-23 21:28:15 +0100;
  • 42ff6d7 Version bump in devel: 1.3.1 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-23 21:29:04 +0100;
  • 598ea79 Updated NEWS file by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-23 21:28:15 +0100;
  • 32bf423 Merge remote-tracking branch 'upstream/master' by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-23 21:19:22 +0100;
  • ee7a480 Added functions to extract summary stats from NCBI genomes and compare them to user-defined assembly stats by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-01-23 21:19:15 +0100;
  • d74c747 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 11:26:59 -0400;
  • 4b086cb 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 11:26:58 -0400;
  • c7b1c75 Changed r-lib/actions version tag in GHA workflow by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-20 17:52:15 +0200;
  • b3c76ac Changed formula for synteny assessment to also consider SFT fit by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-20 10:00:48 +0200;
  • f4e3c31 (origin/RELEASE_3_15, RELEASE_3_15) Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-11 10:35:42 +0200;
  • 2041e80 Bug fix: number of duplications was not matching in elements and of the output by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-11 10:32:10 +0200;
  • 691c44b Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-11 10:32:30 +0200;
  • f9ebcf5 Bug fix: number of duplications was not matching in elements and of the output by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-11 10:32:10 +0200;
  • 5077042 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-26 11:50:51 +0200;
  • 589c87d Added median in assess_orthogroups() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-26 11:48:49 +0200;
  • e86df13 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-26 11:49:25 +0200;
  • ba852cd Added median in assess_orthogroups() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-26 11:48:49 +0200;
  • 48c3e83 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-21 13:38:30 +0200;
  • b1e8e1d Updated NEWS.md and fixed denominator in formula for calculate_H() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-21 13:37:24 +0200;
  • 26097e9 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-21 13:37:41 +0200;
  • bf3a558 Updated NEWS.md and fixed denominator in formula for calculate_H() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-21 13:37:24 +0200;
  • abfaa85 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 21:29:45 +0200;
  • ba08433 Added scale param in calculate_H by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 21:28:07 +0200;
  • be906c4 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 21:28:37 +0200;
  • c7cc084 Added scale param in calculate_H by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 21:28:07 +0200;
  • 211ad9d Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 14:55:14 +0200;
  • aa53b8f Added correction for overclustering in OG assessment and changed color of BUSCO plot for a darker yellow for better visualization by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 14:53:38 +0200;
  • 5bbcf96 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 14:54:01 +0200;
  • 051c777 Added correction for overclustering in OG assessment and changed color of BUSCO plot for a darker yellow for better visualization by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-20 14:53:38 +0200;
  • 6830633 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:34:53 +0200;
  • 4313043 Bug fix: Removed rlang from Imports and fixed undocumented parameter by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:33:29 +0200;
  • e83a916 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:33:58 +0200;
  • 44b6c1f Bug fix: Removed rlang from Imports and fixed undocumented parameter by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:33:29 +0200;
  • 8bd07d4 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:06:58 +0200;
  • d08ff96 Increased test coverage and fixed bug in calculation of homogeneity scores by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:05:02 +0200;
  • ca44062 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:05:37 +0200;
  • d6d6410 Increased test coverage and fixed bug in calculation of homogeneity scores by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-31 17:05:02 +0200;
  • 532acdd bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-27 15:47:35 -0400;
  • 31c9e5b bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-27 15:47:35 -0400;
  • 4373963 Fixed R version in Depends and added a suggested biocViews entry by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-04-20 20:39:19 +0200;
  • fa394fb Added option for DNA/RNA/AAStringSet object in run_busco() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-04-20 18:16:06 +0200;
  • 68339ad Named sessionInfo() code chunk in vignettes 2 and 3 - possible bug in Bioc build system by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-21 20:38:23 +0100;
  • 2edfb82 Added cogeqc to "Watched Tags" in Bioc Support site by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-21 20:21:20 +0100;
  • c391542 Removed interoperability with {Herper} by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-14 18:05:27 +0100;
  • 1366881 Expanded package's description in DESCRIPTION and README by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-13 13:12:12 +0100;
  • 1e3c6c2 Increased test coverage by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-13 10:24:44 +0100;
  • 8ec7473 Included test coverage badge in README by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-13 09:58:50 +0100;
  • 962f898 Set dpi = 100 in all vignettes containing plots by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-13 09:41:58 +0100;
  • d469389 Language revision in vignettes by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-13 09:22:11 +0100;
  • b926af4 Fixed affiliation in vignettes and non-standard evaluation issues by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-13 08:41:32 +0100;
  • 7a188cc Included complete affiliations in vignettes by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-12 12:41:27 +0100;
  • 2832bdc Included function plot_og_sizes() and updated vignette to document its usage by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-03-08 13:56:19 +0100;
  • 4d122c3 Updated citation in README by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-02-01 11:26:43 +0100;
  • 18cb926 Changed bibliography in vignette 03 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-30 12:10:56 +0100;
  • 8762bd5 Fixed Date bug in citation by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-30 12:04:32 +0100;
  • 3f907c5 Fixed Date bug in citation by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-30 12:01:28 +0100;
  • e14f907 Added vignette 03 + Added biocViews + Updated affiliation by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-30 11:55:59 +0100;
  • 4fc86cd Added vignette 02 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-07 20:38:56 -0300;
  • ef2e49d Temporarily removed Windows from GHA by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 21:10:00 -0300;
  • bc26d4e Changed cache version in GHA by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 20:55:46 -0300;
  • 120d5ba Changed GLPK version to 5.0 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 20:49:44 -0300;
  • b459c3b Fixed code to install GLPK by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 20:32:31 -0300;
  • f2e7e0e Changed code to install GLPK from binary by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 20:21:14 -0300;
  • a9b6449 Piped yes with Pacman to install GLPK by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 20:12:56 -0300;
  • d4c44ff Changed shell in Windows GHA by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 20:05:11 -0300;
  • 08b6523 Trial: install GLPK on Windows with Pacman by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 19:41:56 -0300;
  • 049d296 Changed cache version in GHA by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 18:26:21 -0300;
  • 25a9171 Install WinGLPK on GHA by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 18:16:28 -0300;
  • a9b2d7e Fixed code to install WinGLPK on GHA <a href="#2">#2</a> by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 18:14:31 -0300;
  • 894d5e2 Fixed code to install WinGLPK on GHA by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 18:08:11 -0300;
  • 36a650a Added code to install GLPK on Windows GHA by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 17:57:55 -0300;
  • 6275d42 Renamed vignettes 00 and 01 due to error in package check by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 16:10:52 -0300;
  • 2207440 Included vignettes 00 and 01 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-01-06 15:56:32 -0300;
  • 742c475 Added {covr} to Suggests by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2021-12-29 12:33:53 -0300;
  • a9d2353 Included assess_synnet() and assess_synnet_list() with unit tests and example data set synnet.rda + Set testthat, covr and pkgdown in GHA to true by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2021-12-29 12:07:26 -0300;