-
Notifications
You must be signed in to change notification settings - Fork 11
/
README
114 lines (80 loc) · 3.99 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
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
--