Wei-ju Wu
weiju

Organizations

@baliga-lab @codeforsystemsbiology
Aug 23, 2016
@weiju
Aug 23, 2016
weiju commented on issue baliga-lab/pf1010-web#95
@weiju

i don't see anything that would prevent the system from creating any early dates, what I see though is that the date parsing is not working in many…

Aug 23, 2016
@weiju
Can't "X" out/delete system in analysis box
Aug 23, 2016
@weiju
  • @weiju e00b03a
    aqxmap.js: null pointer check
Aug 22, 2016
@weiju
Question: Seeing user's system details ?
Aug 22, 2016
@weiju
Previously available systems not visible for my user ?
Aug 22, 2016
weiju commented on issue baliga-lab/pf1010-web#84
@weiju

Ok, the problem is that the new system is searching the graph for the user's system. By default, these are not available when the user has never lo…

Aug 22, 2016
@weiju
Aug 21, 2016
@weiju
  • @weiju b23c1f0
    fixed DataMatrix class: subtract_with_quantile()
Aug 21, 2016
@weiju
  • @weiju ed4f30e
    centralized the scoring matrix caching
Aug 18, 2016
@weiju
  • @weiju 55aadec
    added a BeautifulSoup4 fallback for missing lxml
Aug 18, 2016
weiju commented on issue baliga-lab/cmonkey2#58
@weiju

if possible, you can also provide me with your input files in our shared /proj/omics4tb folder

Aug 18, 2016
weiju commented on issue baliga-lab/cmonkey2#58
@weiju

could you please do me a favor, set multiprocessing to "False" ? You can do this, e.g. by creating a configuration file config.ini with the contents …

Aug 18, 2016
@weiju
  • @weiju 406229f
    added tests for assembler fixed find_fimo
Aug 17, 2016
@weiju
Aug 16, 2016
@weiju
  • @weiju df7f366
    fix: reading data matrix with numeric row names always maps to string…
Aug 15, 2016
weiju commented on issue baliga-lab/cmonkey2#56
@weiju

so it seems that your R is installed in a way that it is not visible from the command line, maybe you are using RStudio as a Mac OS X app, or somet…

Aug 15, 2016
weiju commented on issue baliga-lab/cmonkey2#57
@weiju

Could you please check if the names match up ? This error occurs when you have gene names and they don't match up directly or indirectly (through t…

Aug 15, 2016
weiju commented on issue baliga-lab/cmonkey2#56
@weiju

It looks like you don't have R in your path, and the problem is when you try to install rpy2, could you try to install rpy2 separately ? Looks like…

Aug 15, 2016
@weiju
executable paths
Aug 15, 2016
weiju commented on issue baliga-lab/cmonkey2#55
@weiju

these error messages come from the meme script, cmonkey2 itself does not have as many shell tool dependencies.

Aug 8, 2016
Aug 8, 2016
@weiju
  • @weiju cab3abd
    updated setup.py and README
Aug 8, 2016
@weiju
  • @weiju 89bf4b4
    cleaned up and tweaked structure for PyPI distribution
Aug 8, 2016
@weiju
Aug 8, 2016
weiju commented on issue baliga-lab/cmonkey2#53
@weiju

This error usually indicates that there are problems somewhere in the naming, in our lab, we had this error with a tuberculosis input set because t…

Aug 5, 2016
@weiju
  • @weiju 223cc26
    moved cmviewer package under cmonkey path
Aug 5, 2016
weiju commented on issue baliga-lab/cmonkey2#53
@weiju

Yes, I am currently restructuring cmonkey2 so it will be able to install through pip or setup tools. It seems the configuration loading was broken …

Aug 5, 2016
@weiju
  • @weiju 1b5623e
    fix: configuration file loading
Aug 4, 2016
@weiju