charlesbreeze/eFORGE

Use charlesbreeze repo instead of jherrero

Update instructions for web install …

Prefer to use a VirtualHost now.

Increase fonts and contrast for readability

Increase fonts, parametrise dPlot size, reorder objects

Add --autoopen options

Clean up code + Fix Bonferroni-by-tissue correction

Adds title to the dPlot and change font to Arial

Keep p-value in natural scale and represent the -log10 in ePlot

Avoid using sed which behaves differently in Mac vs Linux

New vertical lines + labels in dPlot

Fix bug in zscore method

Use zscore method to get the zscore

Add zscore method

Prettify the code, remove some legacy bits

Clean up the code …

- Use single quotes within double-quoted text
- Comment the R code
- Remove deprecated rPlot method
- Simplify the table method
- Other cosmetic fixes

Fix last cosmetic change

Cosmetic change to avoid any overlap between the first cell and the l… …

…egend

FDR correction + similar dPlot and PDF …

The points are now colored according to the q-value instead. Also, the PDF output has changed
to be more similar to the dimple plot. The dimple plot now is also more similar to the PDF
as the cell lines/types are sorted in the same way and the break lines between tissues are
also shown.

Adding B-Y FDR corrected q-values to output file

Merge pull request #12 from jherrero/master …

Fix 27k platform label

Fix 27k plpatform label

Merge pull request #11 from jherrero/master …

New update

Add support for different background labels …

The code is now a little smarter about checking that the background is valid and output the set of
available ones otherwise.

Show error output in a text box for readability

Change pod2usage to die call when too few MVPs

Correct the HTML output when an error occurs …

Both stdout and stderr are redirected to the outut file. Show its content in the Error message.

Merge pull request #10 from jherrero/master …

Changes to support 27k array on the web server

Fix typo

Fix bug in sed command

Add new bkgd option (for 27k array) and re-order input form

Re-order progress statements

Rename mvp_bins to mvp_450k_bins

Clean up the code after merge

27k hash addition …

Modification of eFORGE hash selection to include 27k array as an option
for background (subset of 450k probes that are on the 27k array)

Merge pull request #9 from jherrero/master …

New updates