Bioconductor Code: VariantExperiment

Graph of VariantExperiment

55d5620 (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 11:15:51 -0400;
1e2834f (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 11:15:51 -0400;
2010600 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 11:11:51 -0400;
0c15f68 (origin/RELEASE_3_17, RELEASE_3_17) 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 11:11:51 -0400;
9ee3a84 Merge remote-tracking branch 'remotes/upstream/master' by Qian Liu <qliu7@buffalo.edu> 2023-04-13 16:20:05 -0400;
6f14f1b add BiocStyles to address building error in devel 3.17 by Qian Liu <qliu7@buffalo.edu> 2023-04-13 16:14:09 -0400;
863df82 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 11:20:21 -0400;
94a91ff (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 11:20:21 -0400;
3862bbd 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 15:58:23 +0000;
facc20e (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 15:58:23 +0000;
c6e2a3d 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 16:53:37 +0000;
22c0089 (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 16:53:37 +0000;
c5d4dcb bump version to trigger build by Qian Liu <qliu7@buffalo.edu> 2021-05-24 00:15:17 -0400;
4e2f725 Merge branch 'generalVE' by Qian Liu <qliu7@buffalo.edu> 2021-05-23 23:43:15 -0400;
59d0bc3 Add test functions by Qian Liu <qliu7@buffalo.edu> 2021-05-23 23:25:03 -0400;
c50432a Remove methods that are inherited from SeqVarTools. by Qian Liu <qliu7@buffalo.edu> 2021-05-23 11:47:16 -0400;
30cbfe2 rewrite makeVE* function: by Qian Liu <qliu7@buffalo.edu> 2021-05-22 18:48:38 -0400;
b359901 temp commit to fix non-consistent dim nodes by Qian Liu <qliu7@buffalo.edu> 2021-05-20 10:19:39 -0400;
0790346 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 16:45:33 +0000;
41711c2 (origin/RELEASE_3_13, RELEASE_3_13) 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 16:45:33 +0000;
bf33a98 code tweaks by testing scArray gds data by Qian Liu <qliu7@buffalo.edu> 2021-05-14 12:59:19 -0400;
cf8eb94 Added makeVariantExperimentFromGDS for general gds files. by Qian Liu <qliu7@buffalo.edu> 2021-05-13 12:11:41 -0400;
5c1c5b1 rechecked the makeVEfromGDS functions to be consistent with GDSArray: generalgds branch by Qian Liu <qliu7@buffalo.edu> 2021-05-05 07:43:12 -0400;
2ee0ff0 fix bugs in saveVariantExperiment and add into new gds by Qian Liu <qliu7@buffalo.edu> 2021-04-09 12:21:20 -0400;
2e0e24c (origin/RELEASE_3_12, RELEASE_3_12) fix bugs in saveVariantExperiment and add into new gds by Qian Liu <qliu7@buffalo.edu> 2021-04-09 12:21:20 -0400;
af7870b bump version back to release branch by Qian Liu <qliu7@buffalo.edu> 2021-04-05 16:04:38 -0400;
e5b4186 fixed bugs in GDSArray and VE to enable vignette evaluation by Qian Liu <qliu7@buffalo.edu> 2021-04-05 13:19:06 -0400;
e4e6b20 bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:48:29 -0400;
a279f8d bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:48:29 -0400;
6de38d3 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 19:29:25 +0000;
1c142e9 (origin/RELEASE_3_11, RELEASE_3_11) bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 19:29:25 +0000;
1436a8d update method generics corresponding to SeqArray1.27.16 by Liu <qi31566@C02ZT1A7LVDM.local> 2020-04-20 23:47:47 -0400;
b87ff4d deactivate the VE constructors temporarily for 3d GDSArray issue by Liu <qi31566@C02ZT1A7LVDM.local> 2020-03-30 17:02:05 -0400;
e00e727 git pull to address conflicts in pushing by qian <qliu7@buffalo.edu> 2020-03-05 17:10:04 -0500;
4a424cd update utility functions according to changes in GDSArray, deactivate 'gds/genotype' GDSArray construction temporarily by qian <qliu7@buffalo.edu> 2020-03-05 17:06:12 -0500;
71a84c0 bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:43:38 -0400;
540e1d8 (origin/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to even y prior to creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:11:55 -0400;
109fb13 reversed the previous check of GDSArray class for all assays, with the GDSArray 1.5.3 update! by qian <qliu7@buffalo.edu> 2019-10-08 15:22:06 -0400;
bde5d15 tweaks to fix R CMD check warning. by qian <qliu7@buffalo.edu> 2019-10-07 15:51:50 -0400;
b0c8c6c debug on internal functions to use cbind for class preserve by qian <qliu7@buffalo.edu> 2019-10-03 14:13:38 -0400;
a5bc998 Now checking the class of assays for "DelayedArray" instead of "GDSArray" by qian <qliu7@buffalo.edu> 2019-10-03 11:21:24 -0400;
f68c854 updated vignette for easy cross-reference and a more complete method section. by qian <qliu7@buffalo.edu> 2019-08-14 14:56:14 -0400;
a354f34 update authors field, bump version by qian <qliu7@buffalo.edu> 2019-08-14 11:53:04 -0400;
e9a6439 adding user instruction for navigating vignettes by qian <qliu7@buffalo.edu> 2019-08-14 11:52:02 -0400;
70fca37 efficient coding by qian <qliu7@buffalo.edu> 2019-08-14 11:03:58 -0400;
d09171b rename functions of 'makeSummarizedExperiment...' into 'makeVariantExperiment...' by qian <qliu7@buffalo.edu> 2019-06-13 15:10:30 -0400;
edb7243 address BiocCheck error: add importFrom(IRanges, CharacterList) by qian <qliu7@buffalo.edu> 2019-06-11 11:59:15 -0400;
3d19509 'showAvailable()' now returns CharacterList instead of simple list. by qian <qliu7@buffalo.edu> 2019-06-11 11:40:18 -0400;
c409f09 simple version bump by qian <qliu7@buffalo.edu> 2019-05-06 15:59:42 -0400;
c97198d remove the 'Collate' field by qian <qliu7@buffalo.edu> 2019-05-06 15:52:56 -0400;
703acfe updated NEWS file by qian <qliu7@buffalo.edu> 2019-05-06 15:46:05 -0400;
86531f7 some minor updates before submission by qian <qliu7@buffalo.edu> 2019-05-06 15:39:16 -0400;
5ac5cb1 bumped the vignette entry by qian <qliu7@buffalo.edu> 2019-04-26 16:56:39 -0400;
d9e5dfe bump version for DESCRIPTION and dependencies by qian <qliu7@buffalo.edu> 2019-04-26 16:04:57 -0400;
34e5564 git rm VariantExperiment.Rproj by qian <qliu7@buffalo.edu> 2018-12-20 10:25:59 -0500;
0d9c499 add .Rproj as .gitignore by qian <qliu7@buffalo.edu> 2018-12-19 17:15:23 -0500;
a882c37 add some FIXME tags for future improvement by qian <qliu7@buffalo.edu> 2018-12-19 16:59:49 -0500;
7ab4317 some format changes by qian <qliu7@buffalo.edu> 2018-12-19 16:53:07 -0500;
6405684 add biocView terms, cleanup commented code by Qian Liu <qliu7@buffalo.edu> 2018-09-07 16:20:20 -0400;
f3b51da added webhook, bump version for testing. by Qian Liu <qliu7@buffalo.edu> 2018-09-07 11:17:58 -0400;
2578c4f cleanup commented code. bump version. by Qian Liu <qliu7@buffalo.edu> 2018-09-07 11:09:44 -0400;
b6976d1 update DESCRIPTION for submission by Qian Liu <qliu7@buffalo.edu> 2018-09-06 16:40:13 -0400;
6217f9f merge VCF2VE branch into master by Qian Liu <qliu7@buffalo.edu> 2018-08-07 12:51:32 -0400;
b6230c9 updated vignettes, and added beamer slides under inst/ by Qian Liu <qliu7@buffalo.edu> 2018-07-23 16:17:53 -0400;
b0e8a5b import all SummarizedExperiment; Split vignettes and finished "class" one. by Qian Liu <qliu7@buffalo.edu> 2018-07-05 18:30:00 -0400;
b3c0c23 Function renaming, argument consistency, documentation debugging. by Qian Liu <qliu7@buffalo.edu> 2018-07-05 16:52:27 -0400;
764ab9b tweaks: by Qian Liu <qliu7@buffalo.edu> 2018-07-03 15:50:53 -0400;
09dd6d9 Finished vignette_v1 and some function renaming. by Qian Liu <qliu7@buffalo.edu> 2018-07-03 14:07:25 -0400;
3e0a820 final polishes. by Qian Liu <qliu7@buffalo.edu> 2018-07-02 14:55:54 -0400;
1917d8e tweaks to pass check(). by Qian Liu <qliu7@buffalo.edu> 2018-06-28 18:49:37 -0400;
d2e963f finished tests for VE stats functions. by Qian Liu <qliu7@buffalo.edu> 2018-06-27 12:33:55 -0400;
821784d added test functions for VCF2VE. by Qian Liu <qliu7@buffalo.edu> 2018-06-26 17:46:36 -0400;
e1c8163 successfully tested implemented stats functions on example vcf file. by Qian Liu <qliu7@buffalo.edu> 2018-06-26 16:34:40 -0400;
fb731cd add additional checking and warnings if sample annot does not include all samples. by Qian Liu <qliu7@buffalo.edu> 2018-06-26 15:20:03 -0400;
85c6321 bumped version to 0.2.0 for adding VCF2VE function. by Qian Liu <qliu7@buffalo.edu> 2018-06-26 12:42:43 -0400;
946c86a implemented 'sample.info' argument inside 'VCF2VE' and tested successfully. by Qian Liu <qliu7@buffalo.edu> 2018-06-26 12:19:41 -0400;
a89a1ae Implemented "sample.info" argument. by Qian Liu <qliu7@buffalo.edu> 2018-06-25 17:22:16 -0400;
c644817 Tested that all arguments within "VCF2VE" works. by Qian Liu <qliu7@buffalo.edu> 2018-06-25 12:23:54 -0400;
a291789 testing VCF2VE arguments. (finished before "start=1L") by Qian Liu <qliu7@buffalo.edu> 2018-06-22 17:26:45 -0400;
cd44542 implementation of "VCF2VE" function. by Qian Liu <qliu7@buffalo.edu> 2018-06-22 16:13:12 -0400;
8555573 merged with master. by Qian Liu <qliu7@buffalo.edu> 2018-05-29 14:16:30 -0400;
481ebee merge ddf3rd into master by Qian Liu <qliu7@buffalo.edu> 2018-05-29 14:09:21 -0400;
ae167d1 updated S4Vectors dependency version 0.19.5 for rbind/bindROWS reimplementation by Qian Liu <qliu7@buffalo.edu> 2018-05-29 14:03:14 -0400;
8422b9e Moved DelayedDataFrame out into a separate git repo. by Qian Liu <qliu7@buffalo.edu> 2018-05-11 16:50:58 -0400;
7673e29 review DelayedDataFrame code with Herve & Daniel. by Qian Liu <qliu7@buffalo.edu> 2018-05-11 16:05:55 -0400;
5b9ad49 coercion method from DelayedDataFrame to DataFrame. by Qian Liu <qliu7@buffalo.edu> 2018-05-10 11:49:21 -0400;
59e1e3e WIP: VariantExperiment colData as DelayedDataFrame by Martin Morgan <martin.morgan@roswellpark.org> 2018-05-01 14:57:27 -0400;
981e547 depends on GDSArray 0.9.14 by Qian Liu <qliu7@buffalo.edu> 2018-05-01 10:13:56 -0400;
d158646 Update DESCRIPTION by Qian Liu <qliu7@buffalo.edu> 2018-04-27 14:02:34 -0400;
6b2173b gdsfile() method signature to be object from x; updated GDSArray:::.get_gdsdata_non1D_array instead of .get_gdsdata_arrayNodes by Qian Liu <qliu7@buffalo.edu> 2018-04-26 14:26:00 -0400;
2b4c8eb modified unit tests by Qian Liu <qliu7@buffalo.edu> 2018-04-17 12:35:49 -0400;
2248d8f updated unit test, 'extractROWS,DelayedDataFrame'. by Qian Liu <qliu7@buffalo.edu> 2018-04-17 12:03:13 -0400;
39fa03c updated test,DelayedDataFrame with lazyIndex<-, validityCheck, and constructor over DDF. by Qian Liu <qliu7@buffalo.edu> 2018-04-17 11:49:41 -0400;
b6473a5 DelayedDataFrame constructor and "[" method re-implementation. by Qian Liu <qliu7@buffalo.edu> 2018-04-17 10:23:32 -0400;
8ed8827 modified concatenateObjects,LazyIndex for cumsum of lengths(listData) instead of lengths(indexes) by Qian Liu <qliu7@buffalo.edu> 2018-04-13 15:17:29 -0400;
216f86f resumed the [<-,DDF, and validity check of LazyIndex to working condition. by Qian Liu <qliu7@buffalo.edu> 2018-04-13 13:31:42 -0400;
27703a1 Merge branch 'ddf3rd.bk' into ddf3rd by Qian Liu <qliu7@buffalo.edu> 2018-04-13 11:44:37 -0400;
247f5b5 R CMD CHECK modifications on imports, rdnames... by Qian Liu <qliu7@buffalo.edu> 2018-04-13 11:39:54 -0400;
0bc5b8f added length() method for LazyIndex by Qian Liu <liuqian.pumc@gmail.com> 2018-04-12 16:06:17 -0400;
8ae54a4 update DelayedDataFrame validity method by Martin Morgan <martin.morgan@roswellpark.org> 2018-04-10 11:33:37 -0400;