mdozmorov R.genomerunner issues

mdozmorov / R.genomerunner

Scripts and examples of visualization and analysis of the enrichment and epigenomic similarity results

3 stars 1 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Loading image not showing

#50 lkscara closed 8 years ago
0
Unexplained Shiny hangups

#49 mdozmorov closed 8 years ago
0
Add clustering assignment file to download

#48 mdozmorov opened 9 years ago
0
Bar plot with tooltips

#47 lkscara opened 9 years ago
0
Epigenetic analysis crashing on web server but works on local version

#46 lkscara closed 9 years ago
0
"Download results" zip file contains transformed values in matrix_PVAL_annot.txt (and OR)

#45 mdozmorov closed 9 years ago
1
Enrichment analysis tables - p-values formatting

#44 mdozmorov closed 9 years ago
0
Annotation analysis tab shouldn't have "P-val/FDR/OR" selector

#43 mdozmorov closed 9 years ago
0
Tooltip formatting

#42 mdozmorov closed 9 years ago
1
Long text in cell-specific-analysis table not being truncated

#41 lkscara closed 9 years ago
0
X axis legend tilt like forward slash

#40 mdozmorov closed 9 years ago
0
Remove "P-value multiple testing correction method" from the "Differential regulatory analysis" tab

#39 mdozmorov closed 9 years ago
0
Keep track of required R packages

#38 mdozmorov closed 9 years ago
4
Download button for annotation tables

#37 mdozmorov closed 9 years ago
0
"Download results" tab

#36 mdozmorov closed 9 years ago
2
Add cell type-specific enrichment analysis tab

#35 mdozmorov closed 9 years ago
3
Single-column analysis does not show adjustment option for p-values

#34 mdozmorov closed 9 years ago
2
Annotation analysis results in Shiny

#33 lkscara closed 9 years ago
2
Cut columns in enrichment tables

#32 mdozmorov closed 9 years ago
0
Tooltips on the main heatmap

#31 mdozmorov closed 9 years ago
0
Apply jitter when column values SD is equal to 0 before doing correlation

#30 lkscara closed 9 years ago
0
Heatmap legend use same untransformed values as the y-axis of barplot

#29 lkscara closed 9 years ago
0
Cell type-specific FDR adjustments

#28 mdozmorov closed 9 years ago
0
Breaks when nothing is significant

#27 mdozmorov closed 9 years ago
2
"Download PDF" button missing on Epigenetic similarity heatmap

#26 mdozmorov closed 9 years ago
0
Crashes when height cannot be calculated from the dendrogram

#25 lkscara closed 9 years ago
0
Column names in barplot with '-' breaks for both single and double column

#24 lkscara closed 9 years ago
0
Very large heatmap is never displayed (/Users/mikhail/Documents/Work//VCU_work/Jianlin/data.gr/chr1-23_top/chromStates18/). Can we filter the matrix on the heatmap level to visualize most variable across rows enrichments?

#23 lkscara closed 9 years ago
1
When plotting epigenomic similarity heatmap/changing cluster numbers, we need to skip calculating the results. This adds a notable delay when the matrixes are large. The results should be calculated only when looking at tables.

#22 lkscara closed 9 years ago
1
Packaging dependencies

#21 mdozmorov closed 8 years ago
0
Shiny interface enhancements

#20 mdozmorov closed 9 years ago
0
"Enrichment analysis tables" - everything overrepresented

#19 mdozmorov closed 9 years ago
1
Episimilarity table does not refresh when clustering methods are changed after cluster crashes

#18 lkscara closed 9 years ago
0
One-row matrix error

#17 mdozmorov closed 9 years ago
0
ENCODE database creator

#16 mdozmorov closed 9 years ago
1
Handling when no clusters can be created

#15 mdozmorov closed 9 years ago
0
Heatmap legend title

#14 mdozmorov closed 9 years ago
0
Settings adjustment

#13 mdozmorov closed 9 years ago
0
Add download table buttons

#12 lkscara closed 9 years ago
1
Global control panel

#11 lkscara closed 9 years ago
0
Y axis on barplot

#10 mdozmorov closed 9 years ago
1
OR threshold slider

#9 mdozmorov closed 9 years ago
1
Fixed width of bars on barplot

#8 mdozmorov closed 9 years ago
0
Download button for barplot/heatmap

#7 mdozmorov closed 9 years ago
0
Tables - Copy/Save As buttons for the tables in Shiny

#6 lkscara closed 9 years ago
6
No need in "Select which enrichment table to render" on the Table view - it switched by the combobox on the Barplot view.

#5 lkscara closed 9 years ago
0
GF descriptions in tables: 'enrichment' data frame has 'description' column - merge it to the p-value and OR tables.

#4 lkscara closed 9 years ago
0
Tooltips, next to labels in shiny

#3 lkscara closed 9 years ago
1
Create file path control for loading data when not integrated into GenomeRunner.

#2 lkscara closed 8 years ago
2
Single column barplot visualization adjustments

#1 mdozmorov closed 9 years ago
0