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baliga-lab / cmonkey2

Python port of cMonkey, a machine-learning based method for clustering
GNU Lesser General Public License v3.0
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Resplit based on BSCM in post-processing and fix network load #44

Closed sdanzige closed 9 years ago

sdanzige commented 9 years ago

Two major changes:

1) Resplits clusters in post-processing based on the BSCM p-values if --use_BSCM flag is set. 2) Changes network loading so that stored gene names match those that appear in the ratios matrix. This should deprecate the --remap_network_nodes flag.

Partial Fixes: 1) Resuming works better, but can still have bugs. 2) Parsing the new RSAT directory structure still doesn't work entirely. It fails the Helicobacter_pylori test in run_all_tests.sh

sdanzige commented 9 years ago

When I pulled the merged version from the cMonkey2 repository on a new computer i found some new bugs. I'm working on them now.

-Sam

On Thu, Feb 19, 2015 at 11:37 AM, Wei-ju Wu notifications@github.com wrote:

Merged #44 https://github.com/baliga-lab/cmonkey2/pull/44.

— Reply to this email directly or view it on GitHub https://github.com/baliga-lab/cmonkey2/pull/44#event-238632070.

Samuel A. Danziger, PhD Biomedical Engineering Sam_Danziger@ieee.org (908)246-4502 http://samdanziger.com/

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