Conda and Docker Prep

Updates:

• Readme file updated to include Docker info
• Prep for article submission

Bugfixes:

• Issue #46 , modifies setup.sh for some general installation issues too.

Minor bugfix

Fix for issue #40.

Cleaning and Docker

Minor changes for paper.
Updates:

• Added Dockerfile under the scripts folder.
• Minor Readme updates.
• Clean out .DS_Store files
  Bugfixes:
• matplotlib issue on the Qt backend. See issue #34 .
• urls in setup.sh updated

bioRxiv pre-release version

Final version for the bioRxiv paper.
Updates:

• word cloud resolution modified
• Readme updated
• example "psoriasis" output files for bioRxiv paper included in phenotypeXpression/examples
• gradient legend for heatmap suppressed

Bugfixes:

• setup.sh dependency issues resolved

Batch Effects

Updates:

• Batch effects are now checked in n samples, age of submissions and GPL platform type (all platforms are array types per geoprofiles restrictions)
• Batch effects saved in text file
• Bootstraps increased 1000 -> 5000 to improve reliabilty in clustering, costs about a minute of run time
• dpi on wordcloud increased to 80 -> 200

Now with rpy2!

Draft release that completes using rpy2 instead of independent R.

Updates:

• No longer has same dependencies, can be installed entirely through conda
• Conda version 4.3 or 4.4. Conda 4.5 is experiencing dependency issues
• Pubmed Search now uses broadened HGNC gene names for a wider query volume.

Bugs:

• fixed outprefix to modify file names
• lots more...

Initial pre-release for DOI

Not yet functional, linking to zenodo.