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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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ac1e8a2d49
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Update installation instructions
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2022-01-09 19:54:05 +01:00 |
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283f629696
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ensembl: Save information on species chromosomes
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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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1ec352b1d9
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Update data to Ensembl version 105
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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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8aafcb7555
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clusteriness: Let weights decrease exponentially
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2022-01-04 14:58:49 +01:00 |
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d6ee59af4b
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neural: Increase training time
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2022-01-04 14:58:49 +01:00 |
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1f5909cc02
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plots: Improve scores plot performance
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2022-01-04 14:58:49 +01:00 |
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35fb5e3884
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Add cross-validation function
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2022-01-04 14:58:49 +01:00 |
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83fedfe9be
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neural: Use mean absolute error
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2022-01-04 14:58:49 +01:00 |
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397340cc64
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neural: Use optimizer adam
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2022-01-04 14:58:49 +01:00 |
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8ced026b79
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data: Add more chromosomes
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2021-12-05 19:15:45 +01:00 |
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f940d7d9b0
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plots: Simplify positions plot
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2021-12-03 11:33:51 +01:00 |
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a347bf0ad4
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plots: Refactor and improve
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2021-12-02 17:23:18 +01:00 |
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f997b5fdd7
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plots: Add rankings plot
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2021-12-02 15:28:03 +01:00 |
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2c15ba55c1
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preset: Actually filter input genes
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2021-11-27 12:09:52 +01:00 |
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c6a5c2b59c
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neural: Store the serialized model
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2021-11-27 12:09:52 +01:00 |
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88b1a9ab6a
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Add new method adjacency
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2021-11-27 12:09:52 +01:00 |
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