https://github.com/KoslickiLab/WGSUniFrac

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Revision Author Date Message Commit Date
02e1849 remove more unneeded files 15 June 2022, 19:04:10 UTC
c7a8172 remove unnecessary files 15 June 2022, 18:57:13 UTC
893f0b7 edit readme 23 May 2022, 19:21:58 UTC
e9f22f0 added get_grinder_abundance_for_ogu 13 May 2022, 19:58:06 UTC
08f1044 remove outdated files 04 March 2022, 18:18:06 UTC
4595624 remove load_data.py 04 March 2022, 18:17:11 UTC
c87441c added user manual parts 04 March 2022, 18:15:08 UTC
5a70c8f generate_plot_exp1.py 02 March 2022, 23:02:35 UTC
ab21e88 added get_combined_dataframe_exp1.py, and other related changes 17 February 2022, 19:46:39 UTC
d4b1884 rename 06 February 2022, 18:57:47 UTC
6ee67a8 added qiime script 06 February 2022, 18:53:56 UTC
8bd1455 fixed generate_rawdata_exp1.py and related 31 January 2022, 20:30:38 UTC
0364431 fixed bugs 31 January 2022, 02:18:14 UTC
7da28c8 changed conda install to pip install to install newer version of biom-format 31 January 2022, 02:14:38 UTC
03f44a7 moved saving locationg for the distance file 27 January 2022, 22:09:49 UTC
528aec3 remove secondary files 27 January 2022, 21:53:12 UTC
2f7729b remove run.py 27 January 2022, 21:51:38 UTC
a431a52 remove util.py. No longer needed. 27 January 2022, 21:50:26 UTC
d2005e0 modified generate_rawdata_exp1.py 27 January 2022, 21:47:58 UTC
f249ab0 first commit 27 January 2022, 21:31:21 UTC
b9a8863 update README 23 January 2022, 19:44:04 UTC
4609614 added downloading distance matrix 21 January 2022, 20:55:34 UTC
075c059 Merge branch 'master' of https://github.com/KoslickiLab/WGSUniFrac 20 January 2022, 19:26:44 UTC
d45490d first commit 20 January 2022, 19:22:37 UTC
cebbe25 Update README.md 19 January 2022, 15:44:46 UTC
3966901 Update README.md Test 19 January 2022, 15:43:00 UTC
490bc98 added functions for second part of GTDB 16 November 2021, 00:00:23 UTC
a8cc7b8 added GTDB stuff 01 November 2021, 17:48:08 UTC
462345a added GTDB stuff 01 November 2021, 17:34:38 UTC
23e29b0 first commit 29 August 2021, 21:59:14 UTC
f7de59a . 13 July 2021, 19:34:53 UTC
ad0262a added test_open_profile_from_tsv 13 July 2021, 19:30:35 UTC
6465d6b minor changes in pairwise_unifrac (adjustable branch function) and get_plot_from_xported 06 July 2021, 21:18:09 UTC
88a8cc5 fixed a bug in pairwise_unifrac 03 June 2021, 14:13:43 UTC
43c4926 first commit. Example run: python get_distance_matrix.py -f data/mapping_file2.txt -t data/gg_13_8_otus/trees/99_otus.tree -c 0 -o data/grinder_distance_matrix.txt 20 May 2021, 17:43:57 UTC
3205b4c added functions for read simulation 12 May 2021, 17:51:33 UTC
344c226 first commit 11 May 2021, 04:30:33 UTC
0e7bbab added functions to get data for grinder simulation 20 April 2021, 18:29:30 UTC
053c35b fixed create_data_simple (which resulted in bugs in create_biom) 26 March 2021, 23:55:18 UTC
5d2092e fixed issues in create_profile 26 March 2021, 22:56:46 UTC
65ea8fd first commit 25 March 2021, 17:28:03 UTC
9aa3919 first commit 25 March 2021, 17:26:51 UTC
e93ce53 added plot generating functions 25 March 2021, 17:26:10 UTC
a34e1da fixed create_biom_table and create_profile 25 March 2021, 03:24:24 UTC
b595fe7 first commit 24 March 2021, 19:59:24 UTC
f9e86e8 modified create_profile to get rid of repeated lines 12 March 2021, 23:26:06 UTC
697926c added main 08 March 2021, 22:46:49 UTC
47383fc added run_one function 08 March 2021, 22:24:59 UTC
c514f26 fixed create_data_simple to acommodate merged taxid 03 March 2021, 03:27:34 UTC
9f9ac69 fixed many bugs in create_profile 02 March 2021, 23:48:22 UTC
68a7190 fixed create_profile abundance part 02 March 2021, 04:40:34 UTC
cdc72cc modified create_profile to accommodate abundance 23 February 2021, 17:16:14 UTC
87ab2dd added class Node, create_data_simple, get_distance_dict 23 February 2021, 17:14:53 UTC
d6552ae chaged pick_by_distance function, added get_sorted_distance and test_parallel, setup 14 February 2021, 22:26:30 UTC
cab4797 add 26 January 2021, 21:48:53 UTC
4c4c88c add 23 January 2021, 03:51:49 UTC
2383108 add 23 January 2021, 03:50:10 UTC
c702ba2 add 23 January 2021, 03:48:05 UTC
2e46365 Create README.md 22 January 2021, 18:30:58 UTC
9a0f6fa Merge remote-tracking branch 'origin/master' 22 January 2021, 18:19:53 UTC
773cf85 Delete 99_otu_tree.qza 22 January 2021, 18:19:19 UTC
c91a09b to be runnable from anywhere 22 January 2021, 18:16:30 UTC
c7abd3f Add files via upload 22 January 2021, 17:58:30 UTC
3f2ef1a modified pairwise_unifrac to give plot directly 22 January 2021, 17:10:10 UTC
bc35547 minor changes 22 January 2021, 17:08:35 UTC
6338de9 wasn't there 16 January 2021, 04:44:35 UTC
07d92b7 functionality complete. altered search_by_distance 16 January 2021, 04:44:09 UTC
7c1a846 somehow weighted_unifrac was absent 16 January 2021, 04:43:31 UTC
cb211db added get_plot_from_exported 16 January 2021, 04:42:46 UTC
5232280 added create_data and new ways to pick the nodes. But not ideal still.. much struggling 13 January 2021, 06:01:34 UTC
e5c893e slight modifications here and there. simple test run in main 11 January 2021, 20:41:23 UTC
c950113 Merge remote-tracking branch 'origin/master' 11 January 2021, 04:28:07 UTC
6e51d3d moved auxiliary functions from WGSsimulation.py to utils.py create_biom_table mostly completed (functional) 11 January 2021, 04:26:26 UTC
e58a614 Delete taxdump.tar.gz 10 January 2021, 21:57:31 UTC
17ae346 Delete get_tax_info.py 10 January 2021, 21:57:21 UTC
9ff181a Delete test.py 10 January 2021, 21:56:59 UTC
1fb396a first commit, utilities for WGSUnifrac 10 January 2021, 21:54:10 UTC
028ddcb modified check_rank, filter_id_list, create_profile 10 January 2021, 16:32:44 UTC
f21138c added pick_otu, filter_otus 06 January 2021, 03:51:54 UTC
de4d288 completed pairwise_unifrac 27 December 2020, 23:41:56 UTC
01e985e first commit. One function. pairwise unifrac 04 December 2020, 18:00:49 UTC
d385b40 fixed and renamed filter_id to filter_id_list 31 October 2020, 22:13:48 UTC
e6d5e4a Merge remote-tracking branch 'origin/master' 31 October 2020, 22:00:59 UTC
4adfc31 added filter_id function 31 October 2020, 22:00:46 UTC
4f3706d added data_cleanup.r 30 October 2020, 21:40:27 UTC
daf9646 added taxmap file 30 October 2020, 20:18:53 UTC
13d23e9 added check_rank function 30 October 2020, 19:34:03 UTC
5563e95 added organism_groups and path_and_taxid 30 October 2020, 18:53:55 UTC
35e2f1a Merge remote-tracking branch 'origin/master' 30 October 2020, 18:51:25 UTC
6e4aad6 commit data directory 30 October 2020, 18:50:57 UTC
da18850 Delete .gitkeep 30 October 2020, 18:49:54 UTC
84ec095 Create .gitkeep 30 October 2020, 18:24:14 UTC
68b2f5e added create_profile function 23 October 2020, 18:58:25 UTC
8cd609e first commit 14 October 2020, 23:19:50 UTC
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