METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics
PHP JavaScript Perl Other
Permalink
Failed to load latest commit information.
app Update app/views/dashboard/index.ctp Feb 11, 2013
cake
data udpdated permissions and documentation Jun 28, 2012
db removed kegg_taxon from sqlite (can be created using metarep_update_d… Nov 15, 2012
doc
scripts release 1.4.0 Dec 1, 2012
solr added post.jar Nov 14, 2012
vendors release 1.4.0 Dec 1, 2012
.htaccess new .htaccess Jun 24, 2010
LICENSE.txt release 1.4.0 Dec 1, 2012
README Update README Dec 5, 2012
index.php initial commit Jun 18, 2010

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
--