1. AnnotationForge
  2. Graph
Graph of AnnotationForge
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  • 17653c7 (origin/RELEASE_3_16, RELEASE_3_16) bump version to 1.40.2 by Hervé Pagès <hpages.on.github@gmail.com> 2023-03-25 13:39:02 -0700;
  • 4523ef1 Merge remote-tracking branch 'upstream/RELEASE_3_16' into RELEASE_3_16 by Hervé Pagès <hpages.on.github@gmail.com> 2023-03-25 13:28:14 -0700;
  • 6d91aaa Use dbExecute() instead of dbGetQuery() or dbSendQuery() to avoid warnings by Hervé Pagès <hpages.on.github@gmail.com> 2023-03-25 13:21:47 -0700;
  • e7cd29c (HEAD -> devel, origin/master, origin/devel, origin/HEAD, master) Use dbExecute() instead of dbGetQuery() or dbSendQuery() to avoid warnings by Hervé Pagès <hpages.on.github@gmail.com> 2023-03-25 13:21:47 -0700;
  • 27b4772 Fixed makeOrgPackageFromNCBI to use existing downloaded files. by Jim MacDonald <jmacdon@uw.edu> 2023-02-15 09:23:38 -0800;
  • c4201ca Fixed makeOrgPackageFromNCBI to use existing downloaded files by Jim MacDonald <jmacdon@uw.edu> 2023-02-15 09:19:52 -0800;
  • e247a06 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 11:07:07 -0400;
  • f77d3a9 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 11:07:07 -0400;
  • b313550 Update viableID for release by lshep <lori.shepherd@roswellpark.org> 2022-09-13 07:40:30 -0400;
  • 2dcedf3 (origin/RELEASE_3_15, RELEASE_3_15) version bump 1.38.1 by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-08-10 16:48:13 -0400;
  • 07491cd update uniprot url for XML query by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-08-04 17:56:55 +0000;
  • 9a8f575 Update REST query to changes in uniprot.org by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-08-04 17:44:11 +0000;
  • 3e01d4f version bump 1.39.1 by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-08-04 14:16:10 -0400;
  • 98baa73 update uniprot url for XML query by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-08-04 17:56:55 +0000;
  • 41f4f1c Update REST query to changes in uniprot.org by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-08-04 17:44:11 +0000;
  • 9a476ba 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 15:11:22 +0000;
  • 1f77750 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 15:11:22 +0000;
  • f2e903e update viableID for release 3.15 by lshep <lori.shepherd@roswellpark.org> 2022-04-11 11:33:22 -0400;
  • ea932f3 version bump 1.37.4 by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-03-29 13:14:49 -0400;
  • 852ed89 use bfcrpath to obtain file.path to resource by LiNk-NY <marcel.ramosperez@roswellpark.org> 2022-03-29 13:14:19 -0400;
  • aed6ba0 Fix typo by lshep <lori.shepherd@roswellpark.org> 2022-03-10 11:57:42 -0500;
  • 2f2d03e minor changes to viableID by lshep <lori.shepherd@roswellpark.org> 2022-03-01 10:11:04 -0500;
  • c876e91 Fix size and suggest AnnotationHub Closes <a href="#27">#27</a> by lshep <lori.shepherd@roswellpark.org> 2022-02-24 08:13:33 -0500;
  • 6692449 Add helpful hint for increasing download file timeout limit and space requirement by lshep <lori.shepherd@roswellpark.org> 2022-02-24 08:07:09 -0500;
  • ac8fa56 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 16:03:32 +0000;
  • 523b5f0 (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 16:03:32 +0000;
  • a2fccf4 (origin/RELEASE_3_13, RELEASE_3_13) Bugfix for makeOrgPackageFromNCBI.R. RCurl on Windows uses old version of OpenSSH so we get TLS V1 errors. The download.file function in base R uses libcurl anyway, so we switched to use that instead. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-10-11 16:11:15 -0700;
  • 3e57609 Updates to makeOrgPackageFromNCBI to use download.file instead of RCurl to download files, as RCurl is problematic on Windows. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-10-11 15:59:51 -0700;
  • 378d4d2 Update viableIDs.rda for release by lshep <lori.shepherd@roswellpark.org> 2021-09-23 10:28:50 -0400;
  • b0310ee 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 15:52:48 +0000;
  • ca11ffe 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 15:52:48 +0000;
  • 76d8d97 Fixed DESCRIPTION files in templates to have methods and AnnotationDbi only in Depends line, not Imports as well. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-19 07:44:12 -0700;
  • 29ced4c Updated NEWS and bumped version. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-18 12:03:47 -0700;
  • b5c9220 Merge branch 'master' of github.com:jmacdon/AnnotationForge by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-18 11:52:05 -0700;
  • 09f51ad bumped version by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-18 11:50:39 -0700;
  • 22ee623 Hopefully the last mismatched parenthesis... by Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal> 2021-05-17 23:44:57 +0000;
  • e33a9d5 More extraneous close parentheses... by Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal> 2021-05-17 21:14:07 +0000;
  • 83a9a24 Fixed unmatched parenthesis in CHR.Rd by Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal> 2021-05-17 18:41:41 +0000;
  • 43e57d5 Modifications to help pages to allow larger Affy chips to check - with e.g. the Clariom chips getting all the data as a list is computationally expensive. by Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal> 2021-05-17 15:14:38 +0000;
  • a3774b0 Bumped version. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-14 15:29:34 -0700;
  • 5df13a3 Added GENETYPE.Rd to NCBICHIP.DB template so BiMap would build. by Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal> 2021-05-14 22:27:29 +0000;
  • 635c9ba Changes to vignettes and ChipDb builder to accommodate loss of UniGene table. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-10 15:43:59 -0700;
  • a173ca1 Version bump after merging anno_3_13 branch by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-10 14:32:26 -0700;
  • 2f40df0 Merge branch 'anno_3_13' by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-10 14:28:54 -0700;
  • b12ccaa Fix for .onload where it was trying to make the BiMaps. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 15:02:15 -0700;
  • c2b9c22 More changes to ANNDBPKG-INDEX to accommodate building OrthologyDb package. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 14:55:45 -0700;
  • 7d977e6 Removed organism from DESCRIPTION file for OrthologyDb. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 14:38:42 -0700;
  • 2e59953 Removed organism from DESCRIPTION file for OrthologyDb. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 14:05:14 -0700;
  • 6616f87 More changes to accommodate building OrthologyDb packages. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 13:46:53 -0700;
  • b6942b7 Missed a closing curly brace. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 12:54:15 -0700;
  • afca4a1 Edits so makeAnnDbPkg does not try to get map_metadata from OrthologyDb. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 12:48:38 -0700;
  • e2eb4a0 Merge branch 'anno_3_13' of github.com:jmacdon/AnnotationForge into anno_3_13 by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 12:28:09 -0700;
  • 23e3cdb Changed to ORTHOLOGY.DB template so the build hopefully does not go through the BiMap building process. by James W. MacDonald <jmacdon@uw.edu> 2021-05-06 12:25:36 -0700;
  • 795edf8 Typo in Orthology package name. by Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal> 2021-05-06 18:29:01 +0000;
  • 58b23ae Put Orthology schema back in ANNDBPKG-INDEX.txt by James W. MacDonald <jmacdon@uw.edu> 2021-05-06 11:22:50 -0700;
  • 20cbcd9 Merge branch 'anno_3_13' of github.com:jmacdon/AnnotationForge into anno_3_13 by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-06 10:49:30 -0700;
  • 01ab200 Updated Orthology help page with examples. by Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal> 2021-05-06 17:47:36 +0000;
  • 9f37e08 Merge branch 'master' of git.bioconductor.org:packages/AnnotationForge by Lori Shepherd <lori.shepherd@roswellpark.org> 2021-05-06 11:22:28 -0400;
  • 4245954 Update viableID.R / viableID.rda by Lori Shepherd <lori.shepherd@roswellpark.org> 2021-05-06 11:21:53 -0400;
  • 7128a67 Backing out changes - the Orthology package will be easier if it does not follow the usual paradigm. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-03 15:35:58 -0700;
  • 19f6861 Changed orthology to Orthology by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-03 13:27:24 -0700;
  • 6100cd3 Added orthology db to ANNDBPKG-INDEX by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-05-03 13:15:35 -0700;
  • d60a3c9 More changes to the GENETYPE man page so it gets found. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-27 09:27:39 -0700;
  • c06d76a Added GENETYPE.Rd file to NCBIORG.DB template. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-23 13:10:03 -0700;
  • 60018c4 Removed GENETYPE2EG because there is no point in having that. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-23 09:05:14 -0700;
  • b6532e3 bold instead of italic by Hervé Pagès <hpages.on.github@gmail.com> 2021-04-22 22:15:57 -0700;
  • 35381e2 Changed all dbGetQuery calls that are actually executable statements to dbExecute. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-22 13:18:38 -0700;
  • 43cd1f8 Additional bugfix. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-22 12:46:32 -0700;
  • f15bdae Additional bugfix. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-22 11:44:26 -0700;
  • 0f77be7 Additional bugfix missed in last two commits. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-22 11:23:46 -0700;
  • 77475e7 Additional bugfix missed in last commit. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-22 11:20:23 -0700;
  • e4d1ac1 Bugfix to SQL code to generate genetype tables. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-22 11:14:34 -0700;
  • fd901ad Added appendGenetype function to all the popXXX functions. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-22 10:55:09 -0700;
  • e2dd4de First pass at an orthology DB skeleton. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-21 12:59:27 -0700;
  • 385d7fe Initial changes for the removal of UniGene tables and introduction of gene type tables. by Jim MacDonald <jmacdon@vector.deohs.washington.edu> 2021-04-16 08:54:41 -0700;
  • 3c42c26 version bump by LiNk-NY <mramos09@gmail.com> 2021-02-09 15:29:46 -0500;
  • 9410e89 download and cache file in MakingNewAnnotationPackages.Rnw by LiNk-NY <mramos09@gmail.com> 2021-02-09 15:29:12 -0500;
  • 8d55eb5 version bump by LiNk-NY <mramos09@gmail.com> 2021-02-01 16:44:03 -0500;
  • 876c25d remove deprecated hom.Hs.inp.db examples by LiNk-NY <mramos09@gmail.com> 2021-02-01 16:43:20 -0500;
  • ddd8dc7 Version bump for NonStandardOrgDb update by Lori Shepherd <lori.shepherd@roswellpark.org> 2020-10-30 09:53:07 -0400;
  • 234daea Merge branch 'master' into UpdateNonStandardOrgs by Lori Shepherd <lori.shepherd@roswellpark.org> 2020-10-30 09:47:47 -0400;
  • f13aad8 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 10:46:13 -0400;
  • 3d17c2a (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 10:46:13 -0400;
  • e1cbf6f Add URL and BugReports info to DESCRIPTION file by Hervé Pagès <hpages.on.github@gmail.com> 2020-10-27 04:21:52 -0700;
  • 9e21f9c Add RCurl package designation by Lori Shepherd <lori.shepherd@roswellpark.org> 2020-10-26 11:41:42 -0400;
  • 75bf401 Try writing directly to disk instead of loading in memory first by Lori Shepherd <lori.shepherd@roswellpark.org> 2020-10-26 10:42:57 -0400;
  • 72b0b57 Update viableID.rda for release by Lori Shepherd <lori.shepherd@roswellpark.org> 2020-10-05 13:44:58 -0400;
  • 7382b9a Version bump for issue fixes by Kayla-Morrell <Kayla.Morrell@roswellpark.org> 2020-06-01 17:00:58 -0400;
  • c6b75ec Removal of `.getBlast2GOData()` by Kayla-Morrell <Kayla.Morrell@roswellpark.org> 2020-06-01 16:54:11 -0400;
  • db27514 Fixed bug for map_count query in `.addMapCounts()` by Kayla-Morrell <Kayla.Morrell@roswellpark.org> 2020-06-01 12:04:58 -0400;
  • 3f93a43 (origin/RELEASE_3_11, RELEASE_3_11) version bump for temporary path fix for gene2unigene by lshep <lori.shepherd@roswellpark.org> 2020-04-30 10:29:20 -0400;
  • d3cf690 Temporary fix for path to gene2unigene by lshep <lori.shepherd@roswellpark.org> 2020-04-30 09:51:33 -0400;
  • 915d1fa Version bump for temporary path fix for gene2unigene by lshep <lori.shepherd@roswellpark.org> 2020-04-30 10:27:33 -0400;
  • a252f82 Temporary fix for path to gene2unigene by lshep <lori.shepherd@roswellpark.org> 2020-04-30 09:51:33 -0400;
  • 7e29de9 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 18:30:07 +0000;
  • 3d769b6 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 18:30:07 +0000;
  • 465a4ab Update viableIDs data by lshep <lori.shepherd@roswellpark.org> 2020-04-13 16:17:53 -0400;
  • 6a20485 Changes made for annotation pipeline by Valerie Obenchain <vobencha@gmail.com> 2019-11-21 19:32:55 +0000;
  • 1bd3283 Add troublshooting section for non standard org db generation by lshep <lori.shepherd@roswellpark.org> 2019-11-01 09:30:05 -0400;
  • 8f63be9 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 13:36:15 -0400;