1. syntenet
  2. Graph
Graph of syntenet
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  • 844005b (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 11:42:34 -0400;
  • f3a12b6 (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 11:42:34 -0400;
  • 46d6776 Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 23:22:35 +0200;
  • 3f5d6c0 Delete read_last.Rd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 22:56:40 +0200;
  • 1f130b2 Update NAMESPACE by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 22:55:25 +0200;
  • c949d1c Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 22:54:58 +0200;
  • 1dfb289 Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 22:51:56 +0200;
  • 3b7efe2 Update run_last.Rd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 22:25:59 +0200;
  • ad0f3c0 Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 22:24:39 +0200;
  • 83be5c2 Update run_last.Rd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 22:08:17 +0200;
  • 896cc3e Update run_last.Rd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 21:45:11 +0200;
  • 03ae9b5 Update NEWS.md by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 21:43:13 +0200;
  • 6399b8d Update NEWS.md by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 21:40:52 +0200;
  • 6009035 Update DESCRIPTION by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 21:39:00 +0200;
  • db96703 Update check-bioc.yml by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 21:28:24 +0200;
  • 1317054 Update check-bioc.yml by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 21:21:21 +0200;
  • ea329e6 Update check-bioc.yml by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 21:14:41 +0200;
  • 002bc7b Update syntenet.Rmd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 20:53:59 +0200;
  • e9a629f Update vignette_bibliography.bib by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 20:52:47 +0200;
  • 5738b04 Update test-03_synteny_detection.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 20:46:58 +0200;
  • 1af7872 Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 20:44:43 +0200;
  • 6a53329 Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 20:38:38 +0200;
  • 58ef9ef Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 20:28:47 +0200;
  • 5278c32 Create read_last.Rd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 19:22:44 +0200;
  • 0b2fb67 Create run_last.Rd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 19:21:08 +0200;
  • f12faac Create last_is_installed.Rd by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 19:18:17 +0200;
  • e7b9f97 Update NAMESPACE by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 19:11:02 +0200;
  • 4853963 Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 19:03:08 +0200;
  • 897c07f Update utils.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 18:59:58 +0200;
  • cff4319 Update 03_similarity_searches.R by Kristian Ullrich <ullrich@evolbio.mpg.de> 2023-06-20 18:53:43 +0200;
  • 7536b71 (origin/RELEASE_3_17, RELEASE_3_17) Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-15 11:34:37 +0200;
  • 1154ff1 Bug fix: the MCScan algorithm was not using the correct length for the unique species IDs + included a more stringent pattern matching in intraspecies_synteny() to allow only exact matches by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-15 11:32:51 +0200;
  • fc25e37 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-15 11:33:18 +0200;
  • 90a1aeb Bug fix: the MCScan algorithm was not using the correct length for the unique species IDs + included a more stringent pattern matching in intraspecies_synteny() to allow only exact matches by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-15 11:32:51 +0200;
  • 9c4c317 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-09 11:07:08 +0200;
  • 599db5f Added support for parallelization in synteny detection + added option to remove non-coding genes from annotation list in process_input() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-09 11:04:30 +0200;
  • e85670f Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-09 11:05:13 +0200;
  • 35b8d3e Added support for parallelization in synteny detection + added option to remove non-coding genes from annotation list in process_input() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-06-09 11:04:30 +0200;
  • 7784ba5 Updated NEWS file by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-12 10:39:03 +0200;
  • 5360f26 Updated NEWS file by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-12 10:38:07 +0200;
  • 13447d6 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-12 10:31:43 +0200;
  • 3b951c7 Preserved strand information in the output of process_input() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-12 10:29:53 +0200;
  • aa4b0e6 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-12 10:30:26 +0200;
  • b8b2bf2 Preserved strand information in the output of process_input() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-12 10:29:53 +0200;
  • 1b33316 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-09 18:35:51 +0200;
  • 17d99ca Added function collapse_protein_ids() to replace protein IDs with gene IDs in list of AAStringSet objects by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-09 18:33:57 +0200;
  • 5e8c0b9 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-09 18:34:46 +0200;
  • a6b8bfd Added function collapse_protein_ids() to replace protein IDs with gene IDs in list of AAStringSet objects by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-05-09 18:33:57 +0200;
  • 6f3c876 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 11:38:42 -0400;
  • ca36e0a 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 11:38:42 -0400;
  • a5c89b9 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-04-21 14:14:18 +0200;
  • 3248757 Added options to obtain synteny blocks with parse_collinearity() and included support for IQTREE-2 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-04-21 14:13:04 +0200;
  • 803d01e Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-04-20 14:33:27 +0200;
  • 44819f9 Fixed bug in species ID creation, improved UX of intraspecies and interspecies synteny detection functions, and added functions to facilitate the execution of DIAMOND in the command line by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-04-20 14:32:18 +0200;
  • 72b38a1 (origin/RELEASE_3_16, RELEASE_3_16) Bioconductor branch rename from master to devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-03-14 13:12:53 +0100;
  • 8c0632a Bioconductor branch rename from master to devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-03-14 13:12:53 +0100;
  • 2d45907 Version bump in release by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-02-01 20:16:36 +0100;
  • 59f0a87 Replaced sprintf calls with snprintf in C++ code by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-02-01 20:07:04 +0100;
  • b977712 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-02-01 20:09:42 +0100;
  • ba152dc Replaced sprintf calls with snprintf in C++ code by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2023-02-01 20:07:04 +0100;
  • 9607373 Version bump in release: 1.0.3 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-24 19:18:00 +0100;
  • c43fc96 Bug fix: aes_ was deprecated in ggplot2 3.0.0, so testthat was returning warnings. Replaced aes_ with aes and .data from rlang by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-24 19:12:31 +0100;
  • 2f37c2c Version bump in devel: 1.1.3 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-24 19:16:12 +0100;
  • e707eab Bug fix: aes_ was deprecated in ggplot2 3.0.0, so testthat was returning warnings. Replaced aes_ with aes and .data from rlang by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-24 19:12:31 +0100;
  • 81c76b4 Version bump in release: 1.0.2 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-17 14:34:05 +0100;
  • 955834a Added parameters to allow user-defined clustering functions in plot_profiles and cluster_network and added FAQ item by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-17 14:25:50 +0100;
  • b58f9c8 Version bump in devel: 1.1.2 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-17 14:31:13 +0100;
  • 60a2d98 Added parameters to allow user-defined clustering functions in plot_profiles and cluster_network and added FAQ item by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-17 14:25:50 +0100;
  • 4431e6d Fixed Bioc version in GHA workflow by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 10:18:15 +0100;
  • b49217f Fixed Bioc version in GHA workflow by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 10:18:15 +0100;
  • c10a7f0 Changed Bioc version in GHA workflow by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 09:59:05 +0100;
  • 3a7f634 Changed Bioc version in GHA workflow by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 09:59:05 +0100;
  • ab76565 Version bump in release: 1.0.1 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 09:40:38 +0100;
  • 8488561 Moved distance matrix calculation from phylogenomic_profile to plot_profiles, and added more flexibility for users in plot_profiles (see CHANGELOG for details) by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 09:38:41 +0100;
  • d0e9dc4 Version bump in devel: 1.1.1 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 09:39:18 +0100;
  • 4301e7e Moved distance matrix calculation from phylogenomic_profile to plot_profiles, and added more flexibility for users in plot_profiles (see CHANGELOG for details) by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-11-12 09:38:41 +0100;
  • 94bf40f 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 11:27:11 -0400;
  • 4d2bf7e 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 11:27:11 -0400;
  • 0e331d3 Version bump in devel: 0.99.7 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-06 13:21:36 +0200;
  • fbe11b8 Added helper functions to create input data from FASTA/GFF files + updated vignette by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-06 13:20:59 +0200;
  • d360ca4 Version bump in devel: 0.99.6 by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-05 14:09:47 +0200;
  • c063d2a Added a section in vignette to guide users on how to load FASTA files and GFF files to the R session by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-10-05 14:09:06 +0200;
  • 31c3784 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-29 14:26:01 +0200;
  • 8bf9fb6 Changed distance measure in phylogenomic_profile() and increased test coverage by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-09-29 14:25:10 +0200;
  • 2963c7f Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-11 15:12:06 +0200;
  • 2040372 Expanded package description in DESCRIPTION and added option to run DIAMOND for selected comparisons, intraspecies comparisons only, or interspecies comparisons only by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-11 15:11:06 +0200;
  • ee709e5 Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-05 12:10:22 +0200;
  • 38bb919 fix for cpp warnings by Kristian Ullrich <ullrich@evolbio.mpg.de> 2022-08-05 11:44:39 +0200;
  • d6d636a fix for cpp warnings by Kristian Ullrich <ullrich@evolbio.mpg.de> 2022-08-05 11:05:50 +0200;
  • e26abdf fix for cpp warnings by Kristian Ullrich <ullrich@evolbio.mpg.de> 2022-08-04 10:45:08 +0200;
  • 54fbb9b Version bump in devel by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-02 07:15:17 +0200;
  • dcaf4df Bug fix: replaced mkdir with _mkdir from direct.h on Windows by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-08-02 07:14:22 +0200;
  • 91c1d79 Included changes based on suggestions by Bioc reviewer by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-06-19 11:47:44 +0200;
  • aa25b2a Fixed typo in README by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-05-31 09:00:10 +0200;
  • 9e848ce Reduced dimensions of logo + revised language by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-05-31 08:21:45 +0200;
  • 1b9a13a Added logo + removed automatically generated text from NEWS.md by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-05-30 22:07:40 +0200;
  • 15a06f3 Exported interspecies_synteny() with unit tests by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-05-30 14:49:13 +0200;
  • a43b554 Included unit test for intraspecies_synteny() + Added tests/testthat/*.pdf to .gitignore + Fixed man page for intraspecies_synteny() that was not up to date by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-05-30 13:52:13 +0200;
  • 5f90dc1 Merged Kristian's changes after resolving conflicts with local changes by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-05-30 13:41:34 +0200;
  • 944724b Fixed typo in `annotation` man page and exported intraspecies_synteny() by almeidasilvaf <fabricio_almeidasilva@hotmail.com> 2022-05-30 13:34:32 +0200;