Bioconductor Code: GOSemSim

Graph of GOSemSim

ab9af22 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 09:41:14 -0400;
c4646cf (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 09:41:14 -0400;
cc359af update docs by Guangchuang Yu <guangchuangyu@gmail.com> 2023-09-12 15:06:46 +0800;
2f7e001 Merge pull request <a href="#43">#43</a> from Clearmind777/devel by Guangchuang Yu <guangchuangyu@gmail.com> 2023-09-12 13:51:24 +0800;
eaf5e84 readBlast2go.R revised by Clearmind777 <1263015875@qq.com> 2023-08-31 00:28:37 +0800;
82ed536 TCSScutoff.R revised by Clearmind777 <1263015875@qq.com> 2023-08-31 00:26:17 +0800;
c8f6122 check_installed for tidyr and tidyselect in readBlast2go.R done by Clearmind777 <1263015875@qq.com> 2023-08-27 16:52:00 +0800;
a58a08f check_installed for ROCR in TCSScutoff.R done by Clearmind777 <1263015875@qq.com> 2023-08-27 16:39:09 +0800;
7990f34 blast2go by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-10 23:45:59 +0800;
d8b03de (origin/RELEASE_3_17, RELEASE_3_17) blast2go by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-10 23:38:05 +0800;
047899f tmp by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-10 23:25:52 +0800;
cc2ed22 Merge pull request <a href="#41">#41</a> from yangtcai/read_blast2go by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-10 23:19:24 +0800;
a1387e3 Update readBlast2go.R by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-10 23:18:36 +0800;
66ed3e9 Feat: add new function read_blast2go by yangtcai <yangtcai@gmail.com> 2023-07-10 22:51:02 +0800;
3d54a2a buildGOmap() and read.gaf() by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-10 09:01:35 +0800;
352fd4b switch to devel branch by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-02 00:30:41 +0800;
0f3b810 switch bioc branch by Guangchuang Yu <guangchuangyu@gmail.com> 2023-07-01 23:08:38 +0800;
3ee19e3 bump version by Guangchuang Yu <guangchuangyu@gmail.com> 2023-06-30 17:51:26 +0800;
8f71c84 update docs by Guangchuang Yu <guangchuangyu@gmail.com> 2023-06-30 17:15:09 +0800;
360b1b6 Merge pull request <a href="#40">#40</a> from huerqiang/HPOdb by Guangchuang Yu <guangchuangyu@gmail.com> 2023-06-30 17:04:15 +0800;
e1c0604 merge master by huerqiang <13766876214@163.com> 2023-06-30 14:05:19 +0800;
64b5861 Merge pull request <a href="#4">#4</a> from YuLab-SMU/master by Erqiang Hu <13766876214@163.com> 2023-06-30 13:36:52 +0800;
3a20add add HPO.db by huerqiang <13766876214@163.com> 2023-06-30 13:35:41 +0800;
af0fea8 update bioc version by Guangchuang Yu <guangchuangyu@gmail.com> 2023-05-03 15:34:25 +0800;
589fe5b bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 09:48:06 -0400;
ef3d5a7 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 09:48:05 -0400;
ff5bf57 use MPO.db by huerqianga <13766876214@163.com> 2023-04-09 00:59:37 +0800;
42f963e support MPO.db by huerqianga <13766876214@163.com> 2023-04-06 21:54:01 +0800;
6ba0362 Merge pull request <a href="#3">#3</a> from YuLab-SMU/master by Erqiang Hu <13766876214@163.com> 2023-04-06 15:13:04 +0800;
d60df12 update bioc version by Guangchuang Yu <guangchuangyu@gmail.com> 2022-11-02 10:58:31 +0800;
cbc328f bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:04:15 -0400;
ed7334f (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:04:15 -0400;
37900e7 Merge pull request <a href="#2">#2</a> from YuLab-SMU/master by Erqiang Hu <13766876214@163.com> 2022-10-08 15:54:31 +0800;
a84aa66 bump version by Guangchuang Yu <guangchuangyu@gmail.com> 2022-10-07 10:37:15 +0800;
4f55161 Merge pull request <a href="#37">#37</a> from huerqiang/master by Guangchuang Yu <guangchuangyu@gmail.com> 2022-10-07 09:57:43 +0800;
846b35b use HDO.db by huerqiang <13766876214@163.com> 2022-10-07 01:20:01 +0800;
3f48c82 use DOyulab.db by huerqianga <13766876214@163.com> 2022-07-29 16:12:07 +0800;
fb480b5 Merge pull request <a href="#1">#1</a> from YuLab-SMU/master by Erqiang Hu <13766876214@163.com> 2022-07-29 12:41:31 +0800;
104cead update bioc version by Guangchuang Yu <guangchuangyu@gmail.com> 2022-04-27 14:56:25 +0800;
8c9c247 bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:02:23 +0000;
fd74aeb (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:02:23 +0000;
93e0843 fixed <a href="#36">#36</a> for returning NULL when it should be the input object by Guangchuang Yu <guangchuangyu@gmail.com> 2022-01-10 10:12:55 +0800;
4bb6d02 Merge pull request <a href="#36">#36</a> from Nelson-Gon/eval_parse_not by Guangchuang Yu <guangchuangyu@gmail.com> 2022-01-05 12:13:42 +0800;
2e9fb49 Avoid eval-parse when loading orgDb by NelsonGon <gonzabato@hotmail.com> 2022-01-04 12:39:44 +0100;
cf3cd10 bioc version by Guangchuang Yu <guangchuangyu@gmail.com> 2021-10-28 13:06:32 +0800;
2ebeb2e update bioc version by Guangchuang Yu <guangchuangyu@gmail.com> 2021-10-28 10:03:17 +0800;
783f6ef bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 15:53:22 +0000;
fa82442 (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 15:53:22 +0000;
d5e95a8 update docs by Guangchuang Yu <guangchuangyu@gmail.com> 2021-09-03 09:42:06 +0800;
c009b64 tcss method by Guangchuang Yu <guangchuangyu@gmail.com> 2021-08-02 16:14:21 +0800;
072e5cf preprocess tcss by Guangchuang Yu <guangchuangyu@gmail.com> 2021-07-30 17:43:37 +0800;
d2edfc5 (origin/RELEASE_3_13, RELEASE_3_13) update data by Guangchuang Yu <guangchuangyu@gmail.com> 2021-07-28 14:59:58 +0800;
36bbc7b merge by Guangchuang Yu <guangchuangyu@gmail.com> 2021-07-27 16:51:52 +0800;
054bea6 Merge commit 'refs/pull/35/head' of github.com:YuLab-SMU/GOSemSim by Guangchuang Yu <guangchuangyu@gmail.com> 2021-07-26 15:25:03 +0800;
67ddf6e add "is.na" function to remove those nodes not in GOSemSim's datasets by qibaiqi <1178431277@qq.com> 2021-07-21 17:43:43 +0800;
cdee589 Merge commit 'refs/pull/35/head' of github.com:YuLab-SMU/GOSemSim by Guangchuang Yu <guangchuangyu@gmail.com> 2021-07-20 16:37:04 +0800;
0c75a53 correct link by Guangchuang Yu <guangchuangyu@gmail.com> 2021-07-05 11:37:55 +0800;
39ff09a change name by qibaiqi <1178431277@qq.com> 2021-06-09 21:11:44 +0800;
4273d59 Change 'tcssdata' into a pure list data, names are all GO nodes. For each node, 'tcssdata' contains its elements and their ica value, and its clsuters. by qibaiqi <1178431277@qq.com> 2021-06-09 10:22:57 +0800;
e013039 Once made sure output format and value of each step, some code can be removed. by qibaiqi <1178431277@qq.com> 2021-06-01 21:42:52 +0800;
e07765e undone by qibaiqi <1178431277@qq.com> 2021-05-29 00:21:47 +0800;
899e43f not done by qibaiqi <1178431277@qq.com> 2021-05-29 00:19:45 +0800;
beaf9ab Delete unlist+mapply(SIMPLIFY=FALSE) this waste operation. And limit output of "tcssMethod" to NA or real number. by qibaiqi <1178431277@qq.com> 2021-05-29 00:02:00 +0800;
32e53f6 Limit the output format for mapply to list, then use "unlist" function to transform into vector. by qibaiqi <1178431277@qq.com> 2021-05-28 17:19:53 +0800;
20902fe correct some comments and delete "na.omit" in tcssMethod.R by qibaiqi <1178431277@qq.com> 2021-05-26 23:39:42 +0800;
0c5825b when "sim_value" has no value, return NA instead of NULL by qibaiqi <1178431277@qq.com> 2021-05-24 22:31:26 +0800;
746af61 new release by Guangchuang Yu <guangchuangyu@gmail.com> 2021-05-20 13:56:31 +0800;
377305d bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:42:26 +0000;
6e8a8fd bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:42:26 +0000;
a2cdc4c 改回原来的方法 by qibaiqi <1178431277@qq.com> 2021-05-14 12:05:00 +0800;
00fee51 change tcssdata as a nested structure to save time, data.frame is nested within list by qibaiqi <1178431277@qq.com> 2021-05-14 10:59:22 +0800;
2797100 fixed R check by Guangchuang Yu <guangchuangyu@gmail.com> 2021-04-19 16:04:38 +0800;
24d0309 use "slot" function to get value rather than "@" by qibaiqi <1178431277@qq.com> 2021-03-21 17:02:01 +0800;
c392029 in "computeICT" function, define "num" as term's ICT value with offspring node "NA". add brace; by qibaiqi <1178431277@qq.com> 2021-03-18 19:19:26 +0800;
ef4023e take i_pos as center, get 4 numbers from left and right separately; add "drop = FALSE" for geneSim function by qibaiqi <1178431277@qq.com> 2021-03-18 13:32:06 +0800;
d3dfe32 To tradeoff the runtime and accuracy, all possible cutoffs is selected in two steps, roughly compute first and then refine the result in smaller gap. by qibaiqi <1178431277@qq.com> 2021-03-17 23:41:28 +0800;
d5e594c delete "IEA", drop "IEA" or not has no effect on cutoff selecting by qibaiqi <1178431277@qq.com> 2021-03-17 22:21:52 +0800;
e27acdf change the definition of ICT; replace "e" in "function(e)" with more specific noun by qibaiqi <1178431277@qq.com> 2021-03-17 00:09:46 +0800;
6304c3f replace "number_T" with "nTrue", replace "loca" with "pos"; by qibaiqi <1178431277@qq.com> 2021-03-17 00:06:46 +0800;
00e6d55 check the existence of one value, any(x == a) is faster than %in% by qibaiqi <1178431277@qq.com> 2021-03-16 23:56:47 +0800;
0cd0b38 get ancestors from environment to save time by qibaiqi <1178431277@qq.com> 2021-03-07 18:11:49 +0800;
7f8f226 Change the definition of GO, GO should be all the nodes that have annotation in the assigned species. by qibaiqi <1178431277@qq.com> 2021-03-02 20:09:45 +0800;
67c73ad Make code more readable, use number_T and number_F to replace the two value from filtered_ppidata[, 3]. by qibaiqi <1178431277@qq.com> 2021-03-01 21:03:30 +0800;
726a83f Reduce running time and use && and || for logical value by qibaiqi <1178431277@qq.com> 2021-03-01 00:13:28 +0800;
4bf3ec1 check existence of label by qibaiqi <1178431277@qq.com> 2021-02-07 12:08:01 +0800;
2c667fc remove ambiguous variable names;put the sentence out that both exists in if and else. by qibaiqi <1178431277@qq.com> 2021-02-05 21:54:30 +0800;
5a5a00a Change the requirement for ppidata, the column names are not absolute, instead the type of all three columns are required. by qibaiqi <1178431277@qq.com> 2021-02-05 13:25:03 +0800;
f2933f7 use is.na() and is.infinite(); change get_XX function name; replace "ppidata" with "testdata"; add description for parameter; by qibaiqi <1178431277@qq.com> 2021-02-04 20:47:03 +0800;
0cd78be add stop sentence when no TRUE or no FALSE label in test set. by qibaiqi <1178431277@qq.com> 2021-01-30 22:00:14 +0800;
c1cf52c delete else sentence; abandon loop-within-loop, use mapply and build a matrix; other small problems by qibaiqi <1178431277@qq.com> 2021-01-30 00:27:44 +0800;
ca8e1d4 delete unnecessary "else" code; delte unused parameter "geneAnno"; delete unnecessary loop "vapply"; integrate the calculation step about "meta_maxIC" into a function. by qibaiqi <1178431277@qq.com> 2021-01-27 00:10:15 +0800;
ac7b460 删去else语句，精简代码，by 胡二强师兄指导 by qibaiqi <1178431277@qq.com> 2021-01-20 22:47:15 +0800;
c1d8426 update documentation by qibaiqi <1178431277@qq.com> 2021-01-20 22:33:17 +0800;
ce56202 add documentation, 1.use @noRd, 2. add example for testdata 3. internal functions by qibaiqi <1178431277@qq.com> 2021-01-20 19:25:27 +0800;
b595c4e 删去一些不必要的export，by胡二强师兄 by qibaiqi <1178431277@qq.com> 2021-01-20 14:41:33 +0800;
c4cb738 胡二强师兄的改正 by qibaiqi <1178431277@qq.com> 2021-01-20 11:50:40 +0800;
c99a0c2 delete "sapply", replaced with "lapply" or "vapply" by qibaiqi <1178431277@qq.com> 2021-01-19 22:18:53 +0800;
b831b59 Update TCSScutoff.R by Guangchuang Yu <guangchuangyu@gmail.com> 2021-01-18 10:44:37 +0800;
1f3da91 changes in NAMESPACE by qibaiqi <1178431277@qq.com> 2021-01-17 17:29:50 +0800;
b40c4f5 TCSScutoff.R helps detemine the topological cutoff value for TCSSMethod. by qibaiqi <1178431277@qq.com> 2021-01-17 17:26:10 +0800;