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ab545a415c
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clustering: Expose clusteriness parameters
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2022-06-22 13:40:00 +02:00 |
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c6ca93b009
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Allow customizing method metadata
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2022-06-22 13:40:00 +02:00 |
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0e4f4621ed
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Allow to set relation for cluster size
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2022-06-22 13:40:00 +02:00 |
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fddd0c3fa0
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Fix preset bug when filtering species
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2022-06-22 13:40:00 +02:00 |
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2529f35660
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Allow to limit number of clusters for clusteriness
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2022-06-22 13:40:00 +02:00 |
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3df4ec5d89
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compare: Include confidence intervals
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2022-06-03 17:41:45 +02:00 |
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3217c9bd29
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preset: Filter species in addition to genes
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2022-05-30 13:49:52 +02:00 |
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9e96c54f23
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plots: Decrease marker size for input data plot
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2022-05-28 17:11:53 +02:00 |
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abf78f27d3
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plots: Sort species in input data plot
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2022-05-28 17:01:31 +02:00 |
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d144f490a0
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plots: Switch axes of input data plot
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2022-05-28 16:15:33 +02:00 |
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49981300fb
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neural: Refactor and increase gene requirement
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2022-05-26 19:50:23 +02:00 |
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c04b6337e9
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Reindent code to use just two spaces
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2022-05-26 12:42:19 +02:00 |
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a1e6147466
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Add option to show all chromosomes in positions plot
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2022-05-23 11:40:28 +02:00 |
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d83dfa0574
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Fix and enhance hover info in plots
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2022-05-20 10:12:47 +02:00 |
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b17eb049d1
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Add hover information to positions plot
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2022-05-19 17:09:19 +02:00 |
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e41d02c659
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Implement gene set highlighting in positions plot
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2022-05-18 17:29:35 +02:00 |
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7e53015168
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Add chromosomal positions plot
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2022-05-17 21:48:30 +02:00 |
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9590babb1a
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Add some missing import qualifiers
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2022-05-12 18:43:25 +02:00 |
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5bfd20b6b6
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Update to Ensembl 106
This also introduces some additional columns to the stored data tables.
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2022-04-22 13:21:54 +02:00 |
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2427e8c0c0
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plots: Unify colors
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2022-03-01 15:49:04 +01:00 |
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2fb48be0e3
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proximity: Use median distance by default
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2022-02-24 17:44:04 +01:00 |
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99bc6794b9
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Revert "proximity: Remove method"
This reverts commit ac9894e988.
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2022-02-24 17:39:44 +01:00 |
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54e3b433f7
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analyze: Allow to exclude detailed results
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2022-02-24 15:57:27 +01:00 |
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074902b505
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Use median by default in adjacency methods
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2022-02-24 15:36:07 +01:00 |
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33cc33f81a
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ranking: Remove caching for optimization
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2022-02-24 14:51:15 +01:00 |
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57fc119993
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preset: Fix documentation cross-reference
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2022-02-24 14:43:41 +01:00 |
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7fe07aceec
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correlation: Make summary function customizable
This commit also changes the default behavior to using
`stats::median()`.
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2022-02-24 14:43:41 +01:00 |
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3cedc4fea4
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validate: Update and extend
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2022-01-26 11:38:39 +01:00 |
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016a9ada9d
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comparison: Add more useful information
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2022-01-26 10:56:35 +01:00 |
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c633b17db6
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Rename method source files
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2022-01-26 09:59:44 +01:00 |
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ab61f08d0d
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preset: Filter reference genes and add warnings
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2022-01-19 11:18:27 +01:00 |
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53f955f3da
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Add species adjacency method
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2022-01-19 11:18:27 +01:00 |
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c8f1e522f9
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preset: Make reference genes the first parameter
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2022-01-17 19:52:51 +01:00 |
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8cda3e8e83
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adjacency: Revert to density estimate
This reverts commit 23bb499d3a.
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2022-01-13 18:35:02 +01:00 |
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0087f83247
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plots: Show percentiles on hover in rankings
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2022-01-13 11:39:33 +01:00 |
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fa49a5a887
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correlation: Score based on best correlation
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2022-01-09 21:32:37 +01:00 |
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23bb499d3a
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adjacency: Use median as estimate
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2022-01-09 21:27:30 +01:00 |
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32776469bf
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adjacency: Use minimum difference in distances
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2022-01-09 21:14:30 +01:00 |
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2ceda0691b
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adjacency: Make distance estimation customizable
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2022-01-09 20:21:27 +01:00 |
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ac9894e988
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proximity: Remove method
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2022-01-09 19:54:05 +01:00 |
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910bf85719
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clustering: Reduce default span to 100,000
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2022-01-09 19:54:05 +01:00 |
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04809cdc76
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analyze: Fix issue merging scores
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2022-01-09 19:54:05 +01:00 |
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2e27fbb95c
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plots: Add more information to scores plot hover
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2022-01-09 19:54:05 +01:00 |
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a02f22c218
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plots: Display percentiles in scores plot
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2022-01-09 19:54:05 +01:00 |
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a0dce372b6
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ranking: Compute percentiles
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2022-01-09 19:54:05 +01:00 |
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48ff555e88
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ranking: Cache optimizations
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2022-01-09 19:54:05 +01:00 |
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e2b93babe5
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Restructure classes and their responsibilities
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2022-01-09 19:54:05 +01:00 |
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01ec301d6d
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data: Remove absolute positions
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2022-01-04 14:58:49 +01:00 |
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d98c70a205
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Use inherits() for class checking
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2022-01-04 14:58:49 +01:00 |
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207fc753a7
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adjacency: Fix bug in density computation
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2022-01-04 14:58:49 +01:00 |
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