c6116d363c
Update overall style
2022-12-16 11:44:32 +01:00
373238b4bc
plots: Use branded colors
2022-12-16 11:31:30 +01:00
588bf61673
Fix content styling
2022-12-15 13:14:34 +01:00
78da07e12a
Add API documentation
2022-12-11 21:03:41 +01:00
7f70a0c90b
Add API using plumber
2022-12-11 19:08:22 +01:00
26a209aade
Use two-sided Wilcoxon test
2022-12-11 18:41:34 +01:00
995b31646e
Allow setting a custom default dataset
2022-12-02 15:16:37 +01:00
c14208c2b2
Add GTEx tissues dataset
2022-12-01 21:34:07 +01:00
510fafeb6e
Allow selecting the expression dataset
2022-12-01 21:23:46 +01:00
2f24812c90
Export plot functions
2022-11-30 15:27:00 +01:00
a6f0a64c2c
Use package's ranking function for included data
2022-11-30 14:49:42 +01:00
698ea5086a
Move analysis into the package
2022-11-30 14:32:40 +01:00
d25bb424b1
Update precomputed results
2022-10-07 23:44:16 +02:00
670357f01d
Change sidebar headings
2022-10-07 23:14:29 +02:00
3829154c1e
Use newly computed metrics
2022-10-07 23:14:29 +02:00
c97ee1ca30
Improve gene results tables
2022-08-22 16:22:17 +02:00
e621761fd6
Show relative increase in GSEA
2022-07-22 09:03:13 +02:00
22dedfc843
Add link to g:Profiler
2022-07-22 08:51:05 +02:00
015b51e77c
Require greater values in alternative hypothesis
2022-07-18 13:52:14 +02:00
19b395a564
Reverse axes in distribution plots
2022-07-13 18:32:26 +02:00
aed13425ed
Include trend line in GSEA plot
2022-07-02 23:37:13 +02:00
cc17c13888
Use logarithmic normalization
...
This commit also changes the way the standard deviation and mean
expression are computed in general. Now, samples where the gene is not
expressed at all are excluded before the computation.
2022-07-02 17:52:05 +02:00
af6b5561e4
Use random sample for more than 100 genes
2022-07-01 12:37:07 +02:00
7f67dec72e
Show percentiles in overview plot
2022-06-22 20:23:48 +02:00
1bd5e41c8f
Add additional information page
2022-06-22 19:34:39 +02:00
f341031753
ranking: Fix total weight calculation
2022-06-22 19:09:21 +02:00
51c4847949
ui: Move custom css to toplevel div
2022-06-22 13:57:20 +02:00
27f66d7f35
Add custom genes details table
2022-06-22 12:39:26 +02:00
8a96a6eca9
Update gene data based on the suggested ranking
...
This also exports the ranking function itself for external use.
2022-06-15 10:24:10 +02:00
e290aba9ab
Fix details table data selection
2022-06-14 14:04:39 +02:00
2e3521cbd9
Debounce custom gene selection
2022-06-14 13:50:25 +02:00
add8a4bd76
Compute and display confidence interval
2022-06-06 16:15:31 +02:00
882891da53
Reintroduce mean expression as metric
2022-06-06 15:56:34 +02:00
0ee713a966
Transform mean and sd expression using log
2022-06-06 15:48:24 +02:00
ef1c3caa04
Use virtualselect from shinyWidgets
2022-06-02 19:09:13 +02:00
90c9d18f26
Add gprofiler integration
2022-06-02 10:17:49 +02:00
d1398a10f8
Link to GTEx instead of Ensembl
2022-06-02 09:23:01 +02:00
6fb91e0eff
Structure results using tabs
2022-06-02 09:14:34 +02:00
7f69b26a49
Add outputs for custom genes
2022-05-30 21:59:40 +02:00
5f5670171d
Add gene selector for custom genes
2022-05-30 21:27:18 +02:00
780e608ee1
Remove mean expression from score
2022-05-30 20:25:50 +02:00
d495af011a
Use only one cross sample metric
2022-05-30 20:22:42 +02:00
20faaea93d
Add overview
2022-05-30 20:08:54 +02:00
80d81c572d
Reformat to use two spaces for tabs
2022-05-30 19:32:19 +02:00
6aefa55eb9
Add host parameter
2022-05-12 13:37:53 +02:00
92b5e08dc1
Tweak table rendering
2022-05-12 13:24:27 +02:00
1e666d6fa7
Add note on Ensembl links
2022-05-12 13:06:12 +02:00
b4d758ff03
Include more features
2022-05-12 13:03:13 +02:00
c9b26cc823
Move ranking table and support selection
2022-05-12 12:49:16 +02:00
268bfd6415
Hide above 50 TPM values
2022-05-12 12:27:50 +02:00
