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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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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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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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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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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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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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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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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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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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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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a0dce372b6
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ranking: Compute percentiles
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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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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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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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f2bc4318a2
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Fix some package issues
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2021-11-23 09:42:21 +01:00 |
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255123c74f
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Regenerate documentation
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2021-11-22 14:10:22 +01:00 |
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5a58f457a4
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analyze: Add optimization
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2021-11-19 15:07:15 +01:00 |
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de1c1ed40e
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preset: Remove min_n_species customization
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2021-11-18 14:03:11 +01:00 |
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33056bfa40
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Move species count to analysis
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2021-11-18 14:03:11 +01:00 |
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e28bcaafed
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plots: Add position plot
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2021-11-15 15:12:13 +01:00 |
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19bae34a96
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plots: Add max_rank to score plot
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2021-11-15 09:21:37 +01:00 |
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4dda7fa49e
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ranking: Filter out species with too few species
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2021-11-12 10:25:07 +01:00 |
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910eb06fe9
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analyze: Include preset in result
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2021-11-12 10:16:11 +01:00 |
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6d9511fa2e
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Fix some package issues
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2021-11-06 13:22:57 +01:00 |
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28f9834984
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plots: Move rank plot and add boxplot
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2021-11-06 13:03:36 +01:00 |
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d075380559
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ranking: Add plot method
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2021-11-05 23:05:40 +01:00 |
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f98800f1e0
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Add comparison feature
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2021-11-05 19:08:50 +01:00 |
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4992bb2930
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ranking: Use S3 classes and rename optimize method
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2021-11-05 14:47:33 +01:00 |
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55958e0d85
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preset: Turn into S3 class
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2021-11-03 14:17:39 +01:00 |
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c0a1d965d7
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Add more optimization targets
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2021-10-21 11:42:44 +02:00 |
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064f75ddae
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data: Remove n_species from genes
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2021-10-21 11:42:16 +02:00 |
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37f468658c
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Add framework for progress information
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2021-10-19 15:03:10 +02:00 |
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