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METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics

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README
METAREP DIRECTORIES
/app     web application files
/cake    cake framework files
/data    example datasets
/scripts perl and R scripts
/doc     documentation
/db      relational databases  
/solr    solr/lucene configuration files
/vendors 3rd-party php tools

INSTALLATION AND ADDTIONAL INFORMATION
Please visit the project's wiki page at http://wiki.github.com/jcvi/METAREP
for additional information. The 1.3.2 installation guide can be found at 
https://github.com/jcvi/METAREP/wiki/Installation-Guide-v-1.3.2

VIDEO DOCUMENTATION
5 min overview
http://www.youtube.com/watch?v=DJNjM7LMVWU

web tutorial 
http://www.youtube.com/watch?v=7FPJaPyLjMk&feature=relmfu

implementation details
http://www.youtube.com/watch?v=j0rlTIkvfvI


RELEASE NOTES 
JCVI Metagenomics Reports - Version 1.4.0

New Feature:
METAREP-461 Import dataset option for Admin via project page

METAREP-206 New Blast Page to find homologous sequences in selected datasets, display
and export results

METAREP-460 New Search Page option to search datasets using user defined sequences at
three homology cut-off levels (1E-5, 1E-20 and 1E-50)

METAREP-461 Deprecate common name field in Compare Page (will be replaced with a
high level summary, similar to the View Page Summary tab in the next release)

METAREP-462 Adjust Compare Page Layout for new versions of Chrome/Firefox

METAREP-435 New project link shortcut from user dashboard page project listings

METAREP-434 Select datasets for population creation by filtering datasets based on descriptions

METAREP-437 Updated download file header

METAREP-421 Fisher's Exact Test to compare two datasets (exact test)

METAREP-422 Equality of Proportions Test to compare two datasets (large sample approximation)

METAREP-432 False Discovery Rate calculation and filtering for multiple testing correction

METAREP-424 Compare two pathway maps with log odds ratio and significance color coding (available
for 'Statistical tests (2 datasets)' option on the KEGG pathway level; click on image in the last column)


JCVI Metagenomics Reports - Version 1.3.2 (bug fix release)

Bug Fixes:

METAREP-477 Mosaic Plot option was missing in scripts/r/plots.r 
METAREP-478 Population creation process expected core organization by project ID;
the process was fixed to work with a root level core organization as 
generated by the metarep_loader.pl script. 
--

JCVI Metagenomics Reports - Version 1.3.1

New Feature:
METAREP-391 update viral evidence summary for view page
METAREP-409 update NCBI taxonomy, KEGG, GO, and enzymes:

NCBI taxonomy version 09/30/2011: 280,602 new taxa KEGG version 09/01/2011: 21 new KEGG KO pathways; 1 new KEGG EC pathway Gene Ontology version 09/05/2011

METAREP-407 implement GO slim support for compare page
METAREP-406 implement mosaic plot option for compare page
METAREP-205 sequence export option for search page

Bug Fixes:
METAREP-408 fix compare panel misalignment
--

JCVI Metagenomics Reports - Version 1.2.0

Improvement
METAREP-244 - Increased speed of web page build-up
METAREP-247 - Integrate new METAREP logo into web layout

New Feature
METAREP-228 - Added unresolved taxonomy fractions to Browse APIS pages
METAREP-243 - Search datasets using name based searches for Taxonomy, HMM, Enzymes, GO and KEGG pathway names
METAREP-245 - Added search option to filter Browse Taxonomy/GO/Pathway/EC pages
METAREP-248 - Implemented PHP based load balancing option

Bug Fixes
METAREP-246 - Fix View Download Cache Issue
--

JCVI Metagenomics Reports - Version 1.1.0

New Feature
METAREP-215 - Search all datasets option; generate meta-information summaries
METAREP-217 - Allow users to test METAREP without creating an account
METAREP-218 - Allow distance matrix export for hierarchical clustering, heatmap, mds plots
METAREP-219 - Added color legend to heatmap
METAREP-220 - Fixed search example links in search help dialog
METAREP-221 - Use new radio buttons in compare page to limit selection to project datasets
METAREP-223 - Compare datasets using Wilcoxon Rank Sum Test
METAREP-224 - Ajax support for search dataset pages
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