Bioconductor Code: dStruct

Graph of dStruct

163184d (HEAD -> devel, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:34:02 -0400;
524856f (origin/RELEASE_3_21, RELEASE_3_21) bump x.y.z version to even y prior to creation of RELEASE_3_21 branch by A Wokaty <[email protected]> 2025-04-15 12:34:02 -0400;
32829a3 (origin/master) bump x.y.z version to odd y following creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:01:32 -0400;
86d9f15 (origin/RELEASE_3_20, RELEASE_3_20) bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by J Wokaty <[email protected]> 2024-10-29 11:01:32 -0400;
d23992a bump x.y.z version to odd y following creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:35:30 -0400;
85159c4 (origin/RELEASE_3_19, RELEASE_3_19) bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by J Wokaty <[email protected]> 2024-04-30 11:35:30 -0400;
9996b42 bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <[email protected]> 2023-10-24 11:34:31 -0400;
10bfcdb (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 <[email protected]> 2023-10-24 11:34:31 -0400;
aa81e67 Added tidyverse to suggests by dataMaster-Kris <[email protected]> 2023-05-29 11:04:24 -0700;
dafb2da Resolved merge conflict, bumped version number. by dataMaster-Kris <[email protected]> 2023-05-25 23:39:22 -0700;
d776fda Resolved merge conflict, bumped version number. by dataMaster-Kris <[email protected]> 2023-05-25 23:38:43 -0700;
f773d57 bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <[email protected]> 2023-04-25 11:30:55 -0400;
fd33b43 (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 <[email protected]> 2023-04-25 11:30:55 -0400;
b3af24e Add tidyverse to "Suggests" due to BioC build error by dataMaster-Kris <[email protected]> 2023-04-18 23:48:00 -0700;
451dc00 bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <[email protected]> 2022-11-01 11:25:14 -0400;
d240736 (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 <[email protected]> 2022-11-01 11:25:14 -0400;
9c9c68c bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <[email protected]> 2022-04-26 16:16:48 +0000;
55cd897 (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 <[email protected]> 2022-04-26 16:16:48 +0000;
c296967 Update DESCRIPTION by dataMaster-Kris <[email protected]> 2022-02-15 18:46:10 -0800;
feef6a3 Update README.md by dataMaster-Kris <[email protected]> 2022-02-15 18:41:43 -0800;
805d634 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <[email protected]> 2021-10-26 17:10:53 +0000;
55b954a (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 <[email protected]> 2021-10-26 17:10:53 +0000;
4d57f55 Update README.md by dataMaster-Kris <[email protected]> 2021-07-05 23:31:07 -0700;
0033400 Declared namespace of all global variables after BiocCheck by dataMaster-Kris <[email protected]> 2021-05-22 23:23:41 -0700;
7cf40b6 Declare namespace of all elements within scope of functions such as ggplot2, subset, etc. See https://ggplot2.tidyverse.org/articles/ggplot2-in-packages.html by dataMaster-Kris <[email protected]> 2021-05-22 23:07:14 -0700;
657f512 Polished documentation reflecting the switch to IRanges for some of the tasks by dataMaster-Kris <[email protected]> 2021-05-22 21:14:18 -0700;
b87ca82 Addressed Bioconductor reviewer comment 1. by dataMaster-Kris <[email protected]> 2021-05-22 20:36:16 -0700;
06d198f Addressed Bioconductor reviewer comments 3-4. by dataMaster-Kris <[email protected]> 2021-05-22 14:56:24 -0700;
1fbfd30 Addressed Bioconductor reviewer comments 2, 5-7. by dataMaster-Kris <[email protected]> 2021-05-22 12:25:26 -0700;
c35d6ce Documentation for datasets by dataMaster-Kris <[email protected]> 2021-04-11 19:29:29 -0700;
5eda167 Merge branch 'devel' by dataMaster-Kris <[email protected]> 2021-04-11 19:26:50 -0700;
c33e1e6 Added documentation for lai2019 and wan2014, increased tolerance for tests, bumped version and R dependency by dataMaster-Kris <[email protected]> 2021-04-11 19:23:22 -0700;
40dd0dc Updated README by dataMaster-Kris <[email protected]> 2021-04-07 23:06:06 -0700;
5f77867 Regenerated the documentation files by dataMaster-Kris <[email protected]> 2021-04-07 20:13:19 -0700;
9e0759f Added examples to function documentation by dataMaster-Kris <[email protected]> 2021-04-07 20:05:03 -0700;
9c352d3 Removed call to class() function and added description of output from getRegions by dataMaster-Kris <[email protected]> 2021-04-07 19:18:23 -0700;
eb8ef32 Changed T/F to TRUE/FALSE. Required by BiocCheck by dataMaster-Kris <[email protected]> 2021-04-07 19:07:19 -0700;
ed9a980 Adding HTML of vignette by dataMaster-Kris <[email protected]> 2021-04-07 18:29:47 -0700;
488a147 Update R version dependency based on BiocCheck by dataMaster-Kris <[email protected]> 2021-04-07 18:26:53 -0700;
e5392dc Rename data objects by dataMaster-Kris <[email protected]> 2021-04-07 18:18:21 -0700;
95eb8bc suppress warnings by dataMaster-Kris <[email protected]> 2021-04-07 04:58:59 -0700;
7061f24 Changed all tests and code in vignette to single process, devtools build updates by dataMaster-Kris <[email protected]> 2021-04-07 04:47:29 -0700;
0706d5a Updated README by dataMaster-Kris <[email protected]> 2021-04-07 04:12:05 -0700;
02ff610 Delete unwanted license file by dataMaster-Kris <[email protected]> 2021-04-07 03:59:34 -0700;
7b0094e Delete unwanted project file by dataMaster-Kris <[email protected]> 2021-04-07 03:53:53 -0700;
cf69ac4 Delete unwanted hidden file by dataMaster-Kris <[email protected]> 2021-04-07 03:52:24 -0700;
8cdc2b0 Subset Lai et al. data to keep only a dozen or so transcripts, add other files per Bioconductor guidelines by dataMaster-Kris <[email protected]> 2021-04-07 03:48:23 -0700;
b54a013 Added unit tests and minor edits to the vignette by dataMaster-Kris <[email protected]> 2021-04-07 01:19:22 -0700;
4db7a88 Simplified with a definition of dScore by dataMaster-Kris <[email protected]> 2021-04-04 19:52:34 -0700;
43278b5 Updated object name for function component operating on vector input to the function. The component operating on matrix input is fine. by dataMaster-Kris <[email protected]> 2021-04-04 19:32:28 -0700;
91e220b Updated to ensure both guided and de novo modes of dStructome return result table with rownames as serial natural numbers by dataMaster-Kris <[email protected]> 2021-04-04 08:18:51 -0700;
8488e8c Results from dStruct.guided are now labeled as pval and del_d by dataMaster-Kris <[email protected]> 2021-04-04 08:07:17 -0700;
b436dda Rownames of result from dStructome in the guided mode were not series of integers. Now they are. by dataMaster-Kris <[email protected]> 2021-04-04 08:03:26 -0700;
6343e58 dStruct now reports effect size for each tested region in addition to the p-values. by dataMaster-Kris <[email protected]> 2021-04-04 07:48:47 -0700;
bb6f0f5 Update references by dataMaster-Kris <[email protected]> 2021-04-04 06:32:58 -0700;
63b17a6 Updated vignette by dataMaster-Kris <[email protected]> 2021-03-07 06:06:29 -0800;
9bd866a vignette in progress by dataMaster-Kris <[email protected]> 2021-03-03 08:14:30 -0800;
6c15c2c Vignette in progress by dataMaster-Kris <[email protected]> 2021-02-21 00:57:38 -0800;
88024e9 Corrections to references by dataMaster-Kris <[email protected]> 2021-02-18 00:06:38 -0800;
6c90a56 Added data documentation, vignette in progress by dataMaster-Kris <[email protected]> 2021-02-18 00:02:33 -0800;
4abe090 Fix DESCRIPTION by dataMaster-Kris <[email protected]> 2021-02-17 17:26:22 -0800;
d5ac672 Reorganized main code, added test data and vignette in progress by dataMaster-Kris <[email protected]> 2021-02-17 17:16:47 -0800;
f22a1c8 Update README.md by dataMaster-Kris <[email protected]> 2021-01-25 05:45:03 -0800;
fe020bb Update README.md by dataMaster-Kris <[email protected]> 2021-01-25 05:39:18 -0800;
6529148 Update README.md by AviranLab <[email protected]> 2021-01-25 05:34:14 -0800;
850bf52 Clarified that user can change parameter values by dataMaster-Kris <[email protected]> 2019-10-22 23:38:25 -0700;
cb922ef Clarified that the examples use default values by dataMaster-Kris <[email protected]> 2019-10-22 23:29:36 -0700;
051f450 Updated author info by dataMaster-Kris <[email protected]> 2019-02-25 21:04:29 -0800;
f228def Updated plot_dStructome to specify ggplot functions clearly. by dataMaster-Kris <[email protected]> 2019-01-12 20:28:18 -0800;
6f80d3c Create License by AviranLab <[email protected]> 2019-01-09 09:28:34 -0800;
311ef77 Updated README by dataMaster-Kris <[email protected]> 2019-01-09 07:29:25 -0800;
bd85e9e Updated README by dataMaster-Kris <[email protected]> 2019-01-09 07:28:29 -0800;
8568df1 Updated README by dataMaster-Kris <[email protected]> 2019-01-09 07:27:17 -0800;
ba723cc Updated README by dataMaster-Kris <[email protected]> 2019-01-09 06:02:08 -0800;
faae7fe Updated README, by dataMaster-Kris <[email protected]> 2019-01-09 05:54:38 -0800;
edb7477 Updated README, by dataMaster-Kris <[email protected]> 2019-01-09 05:31:46 -0800;
6ea90f0 Updated README, by dataMaster-Kris <[email protected]> 2019-01-09 05:10:24 -0800;
1238ca0 Deleted old manual. by dataMaster-Kris <[email protected]> 2019-01-09 03:05:31 -0800;
865c4b7 Polished the function descriptions. by dataMaster-Kris <[email protected]> 2019-01-09 02:58:26 -0800;
1d53424 Initial commit by dataMaster-Kris <[email protected]> 2019-01-07 17:07:22 -0800;
02e592e Initial commit by AviranLab <[email protected]> 2019-01-07 16:42:30 -0800;