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• fdf89e8496 Version 1.1.0 main v1.1.0 Elias Projahn 2025-02-23 16:04:44 +01:00
• d584cfe12d plots: Use grey background in scores_by_position Elias Projahn 2025-02-23 16:03:47 +01:00
• e4d1d6203a Correct optional dependencies Elias Projahn 2024-04-26 19:02:08 +02:00
• 0eb36fa592 Version 1.0.1 v1.0.1 Elias Projahn 2024-04-25 22:08:27 +02:00
• 2833e6b520 Add citation Elias Projahn 2024-04-25 22:08:15 +02:00
• 49db49cf1e Release 1.0.0 v1.0.0 Elias Projahn 2024-03-28 20:56:28 +01:00
• 7bf23eb157 preset: Add more error and warning messages Elias Projahn 2024-02-13 17:05:00 +01:00
• 50e2fb260f method: Add context help Elias Projahn 2024-01-31 12:14:55 +01:00
• a3cc6a8796 plots: Make chromosome plot static Elias Projahn 2023-11-11 15:50:37 +01:00
• 57a0a8d0ab clustering: Adapt defaults to publication Elias Projahn 2023-11-11 09:44:00 +01:00
• 25bf762ddb Add chromosomes overview plot Elias Projahn 2023-11-10 14:43:48 +01:00
• 795fe99003 Use ensembl database server instead of biomart Elias Projahn 2023-11-08 12:15:26 +01:00
• 948cb337db plots: Use mean gene position for positions plot Elias Projahn 2023-10-27 14:40:26 +02:00
• c60f6a8aff Remove neural network Elias Projahn 2023-10-14 11:33:19 +02:00
• 44e170f5a6 Small documentation improvements Elias Projahn 2023-09-27 13:24:23 +02:00
• 3e19f53d2a Add dependency on ranger Elias Projahn 2023-09-27 13:22:24 +02:00
• e19f154ab5 Update data to Ensembl 110 Elias Projahn 2023-09-27 13:11:08 +02:00
• b4fb39f8de Require R 4.1 Elias Projahn 2023-09-27 12:57:45 +02:00
• 8cf63d26f6 Add link to geposanui Elias Projahn 2022-11-28 15:57:13 +01:00
• 2b859b55dd adjacency: Combine reference genes first Elias Projahn 2022-08-18 19:14:37 +02:00
• 8cde59c1c7 clustering: Increase default cluster span Elias Projahn 2022-08-18 18:45:33 +02:00
• ba55aa124e plots: Rotate and simplify boxplot Elias Projahn 2022-08-18 11:57:46 +02:00
• c8b94fade8 plots: Improve hoverinfo in correlation plot Elias Projahn 2022-08-17 16:17:22 +02:00
• 0440d5931c plots: Fix colors in scores by position plot Elias Projahn 2022-08-14 17:59:07 +02:00
• aee77e8bb5 distance: Switch from median to density estimate Elias Projahn 2022-08-14 17:50:59 +02:00
• 98ee52b122 plots: Add rankings correlation plot Elias Projahn 2022-08-14 16:20:54 +02:00
• 60dc05f6c6 Namespace all method IDs Elias Projahn 2022-08-12 12:41:56 +02:00
• 038208bfbd Implement random forest model method Elias Projahn 2022-08-11 12:32:57 +02:00
• 6cc9196a0d Rename method proximity to distance Elias Projahn 2022-08-11 12:31:57 +02:00
• 0f53c3e798 Rename method proximity to distance Elias Projahn 2022-08-11 12:39:21 +02:00
• 463faf0fbe plots: Replace max rank with percentile lines Elias Projahn 2022-07-22 09:22:16 +02:00
• 8812c9579f Add ORCID to description Elias Projahn 2022-06-28 13:57:07 +02:00
• 260705785a clusteriness: Remove n_clusters and relation Elias Projahn 2022-06-28 13:31:36 +02:00
• 0ae6836d86 Remove species adjacency method Elias Projahn 2022-06-28 13:06:59 +02:00
• ab545a415c clustering: Expose clusteriness parameters Elias Projahn 2022-06-22 11:24:30 +02:00
• c6ca93b009 Allow customizing method metadata Elias Projahn 2022-06-22 11:20:39 +02:00
• 0e4f4621ed Allow to set relation for cluster size Elias Projahn 2022-06-22 11:05:51 +02:00
• fddd0c3fa0 Fix preset bug when filtering species Elias Projahn 2022-06-20 14:30:51 +02:00
• 2529f35660 Allow to limit number of clusters for clusteriness Elias Projahn 2022-06-16 19:45:59 +02:00
• 3df4ec5d89 compare: Include confidence intervals Elias Projahn 2022-06-03 17:41:45 +02:00
• 3217c9bd29 preset: Filter species in addition to genes Elias Projahn 2022-05-30 13:49:52 +02:00
• 9e96c54f23 plots: Decrease marker size for input data plot Elias Projahn 2022-05-28 17:11:53 +02:00
• abf78f27d3 plots: Sort species in input data plot Elias Projahn 2022-05-28 17:01:31 +02:00
• d144f490a0 plots: Switch axes of input data plot Elias Projahn 2022-05-28 16:15:33 +02:00
• 49981300fb neural: Refactor and increase gene requirement Elias Projahn 2022-05-26 19:50:23 +02:00
• c04b6337e9 Reindent code to use just two spaces Elias Projahn 2022-05-26 12:42:19 +02:00
• a1e6147466 Add option to show all chromosomes in positions plot Elias Projahn 2022-05-23 11:40:28 +02:00
• d83dfa0574 Fix and enhance hover info in plots Elias Projahn 2022-05-20 10:12:47 +02:00
• b17eb049d1 Add hover information to positions plot Elias Projahn 2022-05-19 17:09:19 +02:00
• e41d02c659 Implement gene set highlighting in positions plot Elias Projahn 2022-05-18 17:29:35 +02:00
• 7e53015168 Add chromosomal positions plot Elias Projahn 2022-05-17 21:48:30 +02:00
• 9590babb1a Add some missing import qualifiers Elias Projahn 2022-05-12 18:43:25 +02:00
• bae0723533 Add script to approximate centromere locations centromeres Elias Projahn 2022-04-28 11:01:07 +02:00
• 5bfd20b6b6 Update to Ensembl 106 Elias Projahn 2022-04-22 13:21:54 +02:00
• 2427e8c0c0 plots: Unify colors Elias Projahn 2022-03-01 15:49:04 +01:00
• 2fb48be0e3 proximity: Use median distance by default Elias Projahn 2022-02-24 17:44:04 +01:00
• 99bc6794b9 Revert "proximity: Remove method" Elias Projahn 2022-02-24 17:39:44 +01:00
• 54e3b433f7 analyze: Allow to exclude detailed results Elias Projahn 2022-02-24 15:57:27 +01:00
• 074902b505 Use median by default in adjacency methods Elias Projahn 2022-02-24 15:36:07 +01:00
• 33cc33f81a ranking: Remove caching for optimization Elias Projahn 2022-02-24 14:51:15 +01:00
• 57fc119993 preset: Fix documentation cross-reference Elias Projahn 2022-02-24 14:37:33 +01:00
• 7fe07aceec correlation: Make summary function customizable Elias Projahn 2022-02-24 14:34:18 +01:00
• 3cedc4fea4 validate: Update and extend Elias Projahn 2022-01-26 11:38:39 +01:00
• 016a9ada9d comparison: Add more useful information Elias Projahn 2022-01-26 10:56:35 +01:00
• c633b17db6 Rename method source files Elias Projahn 2022-01-26 09:58:33 +01:00
• ab61f08d0d preset: Filter reference genes and add warnings Elias Projahn 2022-01-17 20:22:50 +01:00
• 53f955f3da Add species adjacency method Elias Projahn 2022-01-17 20:11:07 +01:00
• c8f1e522f9 preset: Make reference genes the first parameter Elias Projahn 2022-01-17 19:52:51 +01:00
• 8cda3e8e83 adjacency: Revert to density estimate Elias Projahn 2022-01-13 18:35:02 +01:00
• 0087f83247 plots: Show percentiles on hover in rankings Elias Projahn 2022-01-13 11:39:33 +01:00
• fa49a5a887 correlation: Score based on best correlation Elias Projahn 2022-01-09 21:32:37 +01:00
• 23bb499d3a adjacency: Use median as estimate Elias Projahn 2022-01-09 21:27:30 +01:00
• 32776469bf adjacency: Use minimum difference in distances Elias Projahn 2022-01-09 20:26:42 +01:00
• 2ceda0691b adjacency: Make distance estimation customizable Elias Projahn 2022-01-09 20:21:27 +01:00
• ac9894e988 proximity: Remove method Elias Projahn 2022-01-09 19:52:47 +01:00
• ac1e8a2d49 Update installation instructions Elias Projahn 2022-01-08 20:05:05 +01:00
• 283f629696 ensembl: Save information on species chromosomes Elias Projahn 2022-01-08 17:54:54 +01:00
• 910bf85719 clustering: Reduce default span to 100,000 Elias Projahn 2022-01-07 17:39:26 +01:00
• 04809cdc76 analyze: Fix issue merging scores Elias Projahn 2022-01-04 14:18:57 +01:00
• 1ec352b1d9 Update data to Ensembl version 105 Elias Projahn 2022-01-03 17:49:45 +01:00
• 2e27fbb95c plots: Add more information to scores plot hover Elias Projahn 2021-12-29 21:15:50 +01:00
• a02f22c218 plots: Display percentiles in scores plot Elias Projahn 2021-12-29 16:23:35 +01:00
• a0dce372b6 ranking: Compute percentiles Elias Projahn 2021-12-29 16:09:18 +01:00
• 48ff555e88 ranking: Cache optimizations Elias Projahn 2021-12-16 13:57:02 +01:00
• e2b93babe5 Restructure classes and their responsibilities Elias Projahn 2021-12-16 13:01:44 +01:00
• 01ec301d6d data: Remove absolute positions Elias Projahn 2021-12-13 10:36:44 +01:00
• d98c70a205 Use inherits() for class checking Elias Projahn 2021-12-13 09:50:45 +01:00
• 207fc753a7 adjacency: Fix bug in density computation Elias Projahn 2021-12-09 15:02:25 +01:00
• 8aafcb7555 clusteriness: Let weights decrease exponentially Elias Projahn 2021-12-08 11:51:32 +01:00
• d6ee59af4b neural: Increase training time Elias Projahn 2021-12-06 11:50:00 +01:00
• 1f5909cc02 plots: Improve scores plot performance Elias Projahn 2021-12-06 11:17:11 +01:00
• 35fb5e3884 Add cross-validation function Elias Projahn 2021-12-06 10:50:18 +01:00
• 83fedfe9be neural: Use mean absolute error Elias Projahn 2021-12-06 10:17:08 +01:00
• 397340cc64 neural: Use optimizer adam Elias Projahn 2021-12-05 19:05:57 +01:00
• 8ced026b79 data: Add more chromosomes Elias Projahn 2021-12-05 13:23:00 +01:00
• f940d7d9b0 plots: Simplify positions plot Elias Projahn 2021-12-03 11:33:51 +01:00
• a347bf0ad4 plots: Refactor and improve Elias Projahn 2021-12-02 17:23:18 +01:00
• f997b5fdd7 plots: Add rankings plot Elias Projahn 2021-12-02 15:28:03 +01:00
• 2c15ba55c1 preset: Actually filter input genes Elias Projahn 2021-11-26 11:41:49 +01:00
• c6a5c2b59c neural: Store the serialized model Elias Projahn 2021-11-26 11:40:54 +01:00