geposanui

johrpan/geposanui

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f08c3a8421 preset editor: Select all species by default Elias Projahn 2021-11-23 16:51:55 +01:00
36ccbd4752 Remove position analysis Elias Projahn 2021-11-22 15:16:27 +01:00
9a285fd91b Add chromosome plot Elias Projahn 2021-11-22 13:54:04 +01:00
8a19a701b1 preset editor: Add optimization for median Elias Projahn 2021-11-21 23:57:03 +01:00
ddf03b870e Merge neural method positions and distances Elias Projahn 2021-11-21 23:56:52 +01:00
d2d1e09858 Move optimization to preset editor Elias Projahn 2021-11-19 15:38:46 +01:00
0d1070cc19 preset editor: Remove species slider Elias Projahn 2021-11-18 14:10:06 +01:00
2926bb4da0 results: Remove scroller extension Elias Projahn 2021-11-17 23:08:20 +01:00
a1807691d5 Move species count to preset Elias Projahn 2021-11-17 22:58:55 +01:00
00fbdcac1f Readd distances for neural method Elias Projahn 2021-11-16 16:28:15 +01:00
d654edb8a3 methods: Allow negative weights Elias Projahn 2021-11-16 15:20:42 +01:00
c009bfa371 scatter plot: Move to geposan Elias Projahn 2021-11-15 15:12:42 +01:00
bc99e358c1 assessment: Show comparison genes Elias Projahn 2021-11-15 14:22:33 +01:00
9b9109b389 preset editor: Simplify and add more options Elias Projahn 2021-11-15 10:22:28 +01:00
b5957262a3 Use plots from geposan Elias Projahn 2021-11-15 09:35:47 +01:00
f485eadaf5 Adapt to geposan changes and add new methods Elias Projahn 2021-11-14 22:34:46 +01:00
9709360d45 Improve species slider performance Elias Projahn 2021-11-02 15:07:04 +01:00
69a8326fbc presets: Improve performance Elias Projahn 2021-11-02 14:42:52 +01:00
766ffa15cb filters: Improve user interface Elias Projahn 2021-11-02 14:28:04 +01:00
b57297dfdf Allow filtering by rank Elias Projahn 2021-11-02 13:41:03 +01:00
667eb8f2a3 Properly set replicative species Elias Projahn 2021-10-21 17:34:53 +02:00
4cf5bff125 Move caching to geposan Elias Projahn 2021-10-21 17:26:28 +02:00
33c8292690 Fix disabling of method sliders Elias Projahn 2021-10-21 16:10:46 +02:00
40cb8e6cbd Add workaround to include java script dependencies Elias Projahn 2021-10-21 15:57:08 +02:00
ca1d0e442a Add preset editor Elias Projahn 2021-10-21 14:56:19 +02:00
365cf13dcb Add more optimization targets Elias Projahn 2021-10-21 11:43:34 +02:00
2aed917478 Add README Elias Projahn 2021-10-20 15:39:15 +02:00
d4611f47cf Convert to R package Elias Projahn 2021-10-20 15:34:52 +02:00
b2e2dbf1af Fix assessment synopsis Elias Projahn 2021-10-20 11:30:32 +02:00
b2402ea997 Compute n_species dynamically Elias Projahn 2021-10-20 11:20:20 +02:00
bf6df6af86 Move methods to separate module Elias Projahn 2021-10-19 16:44:29 +02:00
079deb0faf Add progress indicator for analysis Elias Projahn 2021-10-19 15:05:01 +02:00
dc0265a13f Separate out geposan package Elias Projahn 2021-10-19 14:15:28 +02:00
68354bf808 Reorganize source files and generalize presets Elias Projahn 2021-10-16 21:46:59 +02:00
8104e9bd8a Add optimizer and buttons to disable methods Elias Projahn 2021-10-16 17:02:39 +02:00
529f4a553b Fix issue in rank plot Elias Projahn 2021-10-15 18:33:21 +02:00
7800cc09b4 Add more assessment information Elias Projahn 2021-10-15 15:03:40 +02:00
aaff5878ec Organize output in tabs Elias Projahn 2021-10-15 13:59:00 +02:00
527ba01cc9 Add rank plot Elias Projahn 2021-10-15 13:16:51 +02:00
114193506b Port scatter plot to plotly Elias Projahn 2021-10-15 12:24:28 +02:00
fcd9b4ee05 Rearrange user interface Elias Projahn 2021-10-15 11:46:15 +02:00
7b9a42215e Add new method proximity Elias Projahn 2021-10-15 09:27:35 +02:00
9b0b3c13f5 Generalize method definitions Elias Projahn 2021-10-15 09:26:57 +02:00
d3edeefbe2 Only retrieve assembled chromosomes Elias Projahn 2021-10-11 15:10:03 +02:00
c26e4ff4a3 Add option to penalize missing values Elias Projahn 2021-10-11 11:14:08 +02:00
4222a08b87 Add slider to set required number of species Elias Projahn 2021-10-11 11:08:50 +02:00
48aa46c2c4 input: Only connect to Ensembl if necessary Elias Projahn 2021-10-11 10:17:58 +02:00
d87474e574 Update correlation method Elias Projahn 2021-10-11 10:10:28 +02:00
cd63486f0a clusteriness: Don't penalize missing values yet Elias Projahn 2021-10-11 09:48:48 +02:00
b122f2e240 Optimize clustering for speed Elias Projahn 2021-10-09 14:22:28 +02:00
ae0643741a Add buttons to copy results Elias Projahn 2021-10-07 12:59:04 +02:00
686af3f44b Disable gost by default Elias Projahn 2021-10-07 12:42:36 +02:00
f002758fc8 Add gene set enrichment analysis Elias Projahn 2021-10-07 12:18:47 +02:00
d73908acab Optimize ranking weights Elias Projahn 2021-10-07 11:31:45 +02:00
0aa88119d2 Add experimental neural network Elias Projahn 2021-10-05 18:30:12 +02:00
397b8d0ba2 Base clusteriness on species count Elias Projahn 2021-10-04 09:19:38 +02:00
8b727a0329 Add links to Ensembl for genes Elias Projahn 2021-10-01 09:50:04 +02:00
8fc743fe10 Display score and add cut-off filter Elias Projahn 2021-09-30 13:25:39 +02:00
91c15045cf Add new clusteriness score Elias Projahn 2021-09-30 12:54:40 +02:00
ba7c624705 Enhance progress information Elias Projahn 2021-09-21 16:47:13 +02:00
8e54dacd3d Order data before correlating Elias Projahn 2021-09-19 20:19:20 +02:00
e9c05fdbab Reinclude human into distance data Elias Projahn 2021-09-19 12:07:59 +02:00
22b25c9b83 Fix cluster length slider Elias Projahn 2021-09-19 09:57:27 +02:00
03be4bfe5d Add weighted ranking Elias Projahn 2021-09-18 23:33:37 +02:00
9d6b2e4d50 Add new correlation method Elias Projahn 2021-09-18 23:10:52 +02:00
1cea6c3631 Retrieve input data using biomaRt Elias Projahn 2021-09-16 00:06:54 +02:00
040aabc610 Relayout user interface Elias Projahn 2021-08-29 15:53:31 +02:00
7b06f626b9 Add synopsis of results Elias Projahn 2021-08-29 15:29:34 +02:00
437ae6de84 Include data on TPE-OLD status of genes Elias Projahn 2021-08-29 14:02:37 +02:00
42d8da7e77 Add scrolling to output Elias Projahn 2021-08-29 13:43:14 +02:00
3fd8ef6269 Allow using all species for processing Elias Projahn 2021-08-29 13:25:12 +02:00
b69b3e9d2d Always use the largest cluster Elias Projahn 2021-08-26 14:37:17 +02:00
1c88458ce7 Fix minor issues Elias Projahn 2021-08-26 12:51:43 +02:00
363dee2cbd Enhance scatter plot Elias Projahn 2021-08-26 12:50:03 +02:00
1c43433600 Add basic filters to the UI Elias Projahn 2021-08-26 11:20:50 +02:00
d3151957a3 Add initial gene processing Elias Projahn 2021-08-25 15:01:18 +02:00
fd72b3426c Rename data to input Elias Projahn 2021-08-25 12:03:11 +02:00
129793e055 Include all species Elias Projahn 2021-08-25 12:00:22 +02:00
abab22a907 Add a generic caching function Elias Projahn 2021-08-25 11:59:27 +02:00
400ca776e0 Simplify data format and correct scale labels Elias Projahn 2021-08-16 17:21:01 +02:00
495524a0ac plot: Remove old plotting code Elias Projahn 2021-06-28 16:36:53 +02:00
5d59018b2e Start adding an UI using Shiny Elias Projahn 2021-06-24 22:38:16 +02:00
be696b91a0 input: Remove cache from index Elias Projahn 2021-06-24 22:36:46 +02:00
a50feafcca data: Revert to using data.table Elias Projahn 2021-06-24 22:36:02 +02:00
998009b418 data: Simplify data structure Elias Projahn 2021-06-24 20:20:46 +02:00
914673c79c data: Migrate to tidyverse Elias Projahn 2021-06-21 13:03:26 +02:00
cbc444f20c Initial commit Elias Projahn 2021-06-16 22:01:09 +02:00