|
|
54e3b433f7
|
analyze: Allow to exclude detailed results
|
2022-02-24 15:57:27 +01:00 |
|
|
|
074902b505
|
Use median by default in adjacency methods
|
2022-02-24 15:36:07 +01:00 |
|
|
|
33cc33f81a
|
ranking: Remove caching for optimization
|
2022-02-24 14:51:15 +01:00 |
|
|
|
57fc119993
|
preset: Fix documentation cross-reference
|
2022-02-24 14:43:41 +01:00 |
|
|
|
7fe07aceec
|
correlation: Make summary function customizable
This commit also changes the default behavior to using
`stats::median()`.
|
2022-02-24 14:43:41 +01:00 |
|
|
|
3cedc4fea4
|
validate: Update and extend
|
2022-01-26 11:38:39 +01:00 |
|
|
|
016a9ada9d
|
comparison: Add more useful information
|
2022-01-26 10:56:35 +01:00 |
|
|
|
c633b17db6
|
Rename method source files
|
2022-01-26 09:59:44 +01:00 |
|
|
|
ab61f08d0d
|
preset: Filter reference genes and add warnings
|
2022-01-19 11:18:27 +01:00 |
|
|
|
53f955f3da
|
Add species adjacency method
|
2022-01-19 11:18:27 +01:00 |
|
|
|
c8f1e522f9
|
preset: Make reference genes the first parameter
|
2022-01-17 19:52:51 +01:00 |
|
|
|
8cda3e8e83
|
adjacency: Revert to density estimate
This reverts commit 23bb499d3a.
|
2022-01-13 18:35:02 +01:00 |
|
|
|
0087f83247
|
plots: Show percentiles on hover in rankings
|
2022-01-13 11:39:33 +01:00 |
|
|
|
fa49a5a887
|
correlation: Score based on best correlation
|
2022-01-09 21:32:37 +01:00 |
|
|
|
23bb499d3a
|
adjacency: Use median as estimate
|
2022-01-09 21:27:30 +01:00 |
|
|
|
32776469bf
|
adjacency: Use minimum difference in distances
|
2022-01-09 21:14:30 +01:00 |
|
|
|
2ceda0691b
|
adjacency: Make distance estimation customizable
|
2022-01-09 20:21:27 +01:00 |
|
|
|
ac9894e988
|
proximity: Remove method
|
2022-01-09 19:54:05 +01:00 |
|
|
|
ac1e8a2d49
|
Update installation instructions
|
2022-01-09 19:54:05 +01:00 |
|
|
|
283f629696
|
ensembl: Save information on species chromosomes
|
2022-01-09 19:54:05 +01:00 |
|
|
|
910bf85719
|
clustering: Reduce default span to 100,000
|
2022-01-09 19:54:05 +01:00 |
|
|
|
04809cdc76
|
analyze: Fix issue merging scores
|
2022-01-09 19:54:05 +01:00 |
|
|
|
1ec352b1d9
|
Update data to Ensembl version 105
|
2022-01-09 19:54:05 +01:00 |
|
|
|
2e27fbb95c
|
plots: Add more information to scores plot hover
|
2022-01-09 19:54:05 +01:00 |
|
|
|
a02f22c218
|
plots: Display percentiles in scores plot
|
2022-01-09 19:54:05 +01:00 |
|
|
|
a0dce372b6
|
ranking: Compute percentiles
|
2022-01-09 19:54:05 +01:00 |
|
|
|
48ff555e88
|
ranking: Cache optimizations
|
2022-01-09 19:54:05 +01:00 |
|
|
|
e2b93babe5
|
Restructure classes and their responsibilities
|
2022-01-09 19:54:05 +01:00 |
|
|
|
01ec301d6d
|
data: Remove absolute positions
|
2022-01-04 14:58:49 +01:00 |
|
|
|
d98c70a205
|
Use inherits() for class checking
|
2022-01-04 14:58:49 +01:00 |
|
|
|
207fc753a7
|
adjacency: Fix bug in density computation
|
2022-01-04 14:58:49 +01:00 |
|
|
|
8aafcb7555
|
clusteriness: Let weights decrease exponentially
|
2022-01-04 14:58:49 +01:00 |
|
|
|
d6ee59af4b
|
neural: Increase training time
|
2022-01-04 14:58:49 +01:00 |
|
|
|
1f5909cc02
|
plots: Improve scores plot performance
|
2022-01-04 14:58:49 +01:00 |
|
|
|
35fb5e3884
|
Add cross-validation function
|
2022-01-04 14:58:49 +01:00 |
|
|
|
83fedfe9be
|
neural: Use mean absolute error
|
2022-01-04 14:58:49 +01:00 |
|
|
|
397340cc64
|
neural: Use optimizer adam
|
2022-01-04 14:58:49 +01:00 |
|
|
|
8ced026b79
|
data: Add more chromosomes
|
2021-12-05 19:15:45 +01:00 |
|
|
|
f940d7d9b0
|
plots: Simplify positions plot
|
2021-12-03 11:33:51 +01:00 |
|
|
|
a347bf0ad4
|
plots: Refactor and improve
|
2021-12-02 17:23:18 +01:00 |
|
|
|
f997b5fdd7
|
plots: Add rankings plot
|
2021-12-02 15:28:03 +01:00 |
|
|
|
2c15ba55c1
|
preset: Actually filter input genes
|
2021-11-27 12:09:52 +01:00 |
|
|
|
c6a5c2b59c
|
neural: Store the serialized model
|
2021-11-27 12:09:52 +01:00 |
|
|
|
88b1a9ab6a
|
Add new method adjacency
|
2021-11-27 12:09:52 +01:00 |
|
|
|
b1eff374b3
|
Relicense to AGPL
|
2021-11-25 11:16:07 +01:00 |
|
|
|
c0e2dfced2
|
neural: Validate models and store training data
|
2021-11-23 16:26:04 +01:00 |
|
|
|
7c87788cad
|
neural: Use tensorflow seed
|
2021-11-23 11:08:21 +01:00 |
|
|
|
51e7176a1a
|
Store more method results
|
2021-11-23 09:56:02 +01:00 |
|
|
|
f2bc4318a2
|
Fix some package issues
|
2021-11-23 09:42:21 +01:00 |
|
|
|
599f09a52f
|
Remove position analysis
|
2021-11-22 15:16:05 +01:00 |
|
