Bioconductor Code: Browse

Graph ofDIAlignR

5a0da36 (HEAD -> master, origin/master, origin/HEAD) 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 11:21:15 -0400;
96343cb (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 11:21:15 -0400;
ef7e021 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 16:02:14 +0000;
fb216bf (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 16:02:14 +0000;
f028452 [Doc] Updated vignette for three multi-run alignment by Shubham <sgupt46@alumni.uwo.ca> 2022-04-19 12:58:10 -0400;
3ff618b [Feature] Get subset of chromatograms by Shubham <sgupt46@alumni.uwo.ca> 2022-04-19 06:52:07 -0400;
1629bca Merge branch 'master' of github.com:shubham1637/DIAlignR by Shubham <sgupt46@alumni.uwo.ca> 2022-04-19 05:26:12 -0400;
878e445 [Feature] Code to parallelize MST. Code to get MS1 chromatograms by Shubham <sgupt46@alumni.uwo.ca> 2022-04-19 05:16:45 -0400;
0dfa86f Merge branch 'singjc-feature/docker' by Shubham <sgupt46@alumni.uwo.ca> 2022-03-11 12:11:15 -0500;
70f4c31 Merge branch 'feature/docker' of https://github.com/singjc/DIAlignR into singjc-feature/docker by Shubham <sgupt46@alumni.uwo.ca> 2022-03-11 12:11:00 -0500;
1cf0673 BugFix by Shubham <sgupt46@alumni.uwo.ca> 2021-12-29 10:26:38 -0500;
74fff74 [BugFix] Chromatogram merging is one signal has NaN by Shubham <sgupt46@alumni.uwo.ca> 2021-12-23 11:51:09 -0500;
8f4987e [Fix] Added fileInfo2 for progressive alignment by Shubham <sgupt46@alumni.uwo.ca> 2021-12-20 22:48:58 -0500;
76adcc1 minor by Shubham <sgupt46@alumni.uwo.ca> 2021-12-12 14:22:39 -0500;
d3a202a minor by Shubham <sgupt46@alumni.uwo.ca> 2021-12-11 02:51:26 -0500;
15224b2 minor by Shubham <sgupt46@alumni.uwo.ca> 2021-12-10 19:23:57 -0500;
c56de5e [Fix] Fixed hierarchical tree for group-level clustering by Shubham <sgupt46@alumni.uwo.ca> 2021-12-09 21:03:18 -0500;
47596e5 [Fix] Extended support for separate peptide score file by Shubham <sgupt46@alumni.uwo.ca> 2021-12-08 23:42:43 -0500;
a0b770b [BugFix] by Shubham <sgupt46@alumni.uwo.ca> 2021-12-08 21:01:21 -0500;
af08284 [BugFix] by Shubham <sgupt46@alumni.uwo.ca> 2021-12-08 20:43:00 -0500;
e89b5a9 [Fix] Added support for separate peptide score file by Shubham <sgupt46@alumni.uwo.ca> 2021-12-08 13:39:29 -0500;
115ba2c minor by Shubham <sgupt46@alumni.uwo.ca> 2021-10-26 13:52:13 -0400;
875b2ac Merge branch 'master' of git.bioconductor.org:packages/DIAlignR by Shubham <sgupt46@alumni.uwo.ca> 2021-10-26 13:49:34 -0400;
377b51f [Fix] Added defaults in case-switch by Shubham <sgupt46@alumni.uwo.ca> 2021-10-26 13:49:20 -0400;
a8f3e31 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 16:57:00 +0000;
c3e29e4 (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 16:57:00 +0000;
fa60483 [Fix] merged run names by Shubham <sgupt46@alumni.uwo.ca> 2021-10-23 01:36:58 -0400;
e9b4be8 minor by Shubham <sgupt46@alumni.uwo.ca> 2021-10-19 16:36:31 -0400;
81dc639 [BugFix] Tests were failing on windows machine by Shubham <sgupt46@alumni.uwo.ca> 2021-10-19 16:21:36 -0400;
ae4b5de Updated Version by Shubham <sgupt46@alumni.uwo.ca> 2021-10-19 11:26:40 -0400;
c620f7c [Fix] Added fractionation for MST by Shubham <sgupt46@alumni.uwo.ca> 2021-10-19 10:45:32 -0400;
438898c minor by Shubham <sgupt46@alumni.uwo.ca> 2021-10-13 21:06:55 -0400;
55a7ed5 [Bioc] Warning fix by Shubham <sgupt46@alumni.uwo.ca> 2021-10-13 20:06:48 -0400;
18ee125 [TestFix] Removed AsIs operator. Needed in data.frame but not in data.table by Shubham <sgupt46@alumni.uwo.ca> 2021-10-10 10:12:51 -0400;
2052af7 minor by Shubham <sgupt46@alumni.uwo.ca> 2021-09-26 19:50:57 -0400;
4120704 [Feature] Define tree based on batches/cases by Shubham <sgupt46@alumni.uwo.ca> 2021-09-26 19:46:39 -0400;
c652924 [Feature] Added alignToRoot for 100+ runs by Shubham <sgupt46@alumni.uwo.ca> 2021-09-25 16:00:15 -0400;
5f2aa47 [Tests] Fixed tests for the new changes by Shubham <sgupt46@alumni.uwo.ca> 2021-09-25 00:03:37 -0400;
4d13a06 BugFix by Shubham <sgupt46@alumni.uwo.ca> 2021-09-23 18:01:02 -0400;
a939b04 [UPDATE] Add Dockerfile, Rscript folder and snakemake folder to .Rbuildignore by singjc <justincsing@gmail.com> 2021-09-22 01:42:48 -0400;
ff435e7 [Doc] Updated documentation by Shubham <sgupt46@alumni.uwo.ca> 2021-09-20 13:11:43 -0400;
5246fc4 minor by Shubham <sgupt46@alumni.uwo.ca> 2021-09-20 13:11:00 -0400;
882e0ec [Feature] Added tree-distance and tree agglomeration for MST and progressive alignment by Shubham <sgupt46@alumni.uwo.ca> 2021-09-20 13:08:13 -0400;
ae165da [Feature] Added support for direct alignment to the root by Shubham <sgupt46@alumni.uwo.ca> 2021-09-20 13:07:12 -0400;
c137f3a [BugFix] Filter peaks before calculating overlap by Shubham <sgupt46@alumni.uwo.ca> 2021-09-20 13:05:57 -0400;
e86ab64 [BugFix] In case of same m-score, use intensity to assign peak rank. by Shubham <sgupt46@alumni.uwo.ca> 2021-09-20 13:03:51 -0400;
8a86960 [ADD] Add docker badges to README by singjc <justincsing@gmail.com> 2021-08-27 13:54:46 -0400;
d774bcb [ADD] Add docker badges to README by singjc <justincsing@gmail.com> 2021-08-27 13:37:34 -0400;
6aabcc4 [ADD] Add Rcompression install to Dockerfile by singjc <justincsing@gmail.com> 2021-08-27 13:26:38 -0400;
031b854 [ADD] Add Rcompression install to Dockerfile by singjc <justincsing@gmail.com> 2021-08-27 13:01:01 -0400;
16076b0 [UPDATE] Update README with Docker and Snakemake commands by singjc <justincsing@gmail.com> 2021-08-27 12:59:06 -0400;
ff291c7 [UPDATE] Update README with Docker and Snakemake commands by singjc <justincsing@gmail.com> 2021-08-27 12:56:42 -0400;
a43ab18 [ADD] Add comments to snakefile by singjc <justincsing@gmail.com> 2021-08-27 12:49:25 -0400;
382ce85 [ADD] Added snakemake workflow by singjc <justincsing@gmail.com> 2021-08-27 12:36:59 -0400;
3e9d033 [FIX] Replace DialignR install frrom github repo to BioConductor by singjc <justincsing@gmail.com> 2021-08-27 12:05:20 -0400;
619aeab [ADD] Add necessary libs for R packages by singjc <justincsing@gmail.com> 2021-08-27 11:16:47 -0400;
655febc [ADD] Add .dockerignore file to avoid extremely large images by singjc <justincsing@gmail.com> 2021-08-27 09:50:54 -0400;
f18ed0f [ADD] Add Dockerfile and command line Rscript by singjc <justincsing@gmail.com> 2021-08-27 03:40:45 -0400;
4254481 [Feature] intensity calculation for given peaks by Shubham <sgupt46@alumni.uwo.ca> 2021-08-11 23:39:48 -0400;
7621683 Bug fIX by Shubham <sgupt46@alumni.uwo.ca> 2021-08-07 18:18:13 -0400;
73bad4d [Fix] devtools::check() error by Shubham <sgupt46@alumni.uwo.ca> 2021-08-07 12:24:31 -0400;
96e6eda [Fix] default value of samples4gradient by Shubham <sgupt46@alumni.uwo.ca> 2021-08-05 18:27:04 -0400;
a453d7f Merge pull request <a href="#17">#17</a> from singjc/fix/test_ipfReassignFDR by Shubham Gupta <shubham1637@users.noreply.github.com> 2021-07-28 14:28:04 -0400;
c4a5395 [FIX] Fix tests for ptms test and use liner fit instead of loess fit by singjc <justincsing@gmail.com> 2021-07-28 14:23:08 -0400;
263dc39 [Fix] RSE is fixed for two-point alignment by Shubham <sgupt46@alumni.uwo.ca> 2021-07-26 14:58:29 -0400;
f9ff619 [Fix] testcase for new constraining method by Shubham <sgupt46@alumni.uwo.ca> 2021-07-22 20:35:59 -0400;
143675d [Fix] Constraining similarity matrix around non-linearly fit by Shubham <sgupt46@alumni.uwo.ca> 2021-07-20 19:30:35 -0400;
f8b6c4f [Feature] Global alignment is supported and forced alignment is supported by Shubham <sgupt46@alumni.uwo.ca> 2021-07-16 01:14:53 -0400;
05647bd [Fix] Peak picking for out of chromatogram alignment by Shubham <sgupt46@alumni.uwo.ca> 2021-07-10 19:27:54 -0400;
343e6c5 minor by Shubham <sgupt46@alumni.uwo.ca> 2021-07-10 10:34:39 -0400;
143fa08 [ADD] Shrink ptms test files by Shubham <sgupt46@alumni.uwo.ca> 2021-07-09 17:08:02 -0400;
f04d19a [FIX] removed large xics and osw commit by Justin Sing <justincsing@gmail.com> 2021-06-23 18:40:22 -0400;
28ce409 [ADD] Add runType definition to getMultiPeptide by Justin Sing <justincsing@gmail.com> 2021-06-19 01:25:54 -0400;
0b01153 [FIX] fix typo in align_dia_runs, fix data.table import for := in ipfReassignFDR, fix test errors by adding maxIPFFdrQuery to other scripts that use getFeatures by Justin Sing <justincsing@gmail.com> 2021-06-17 11:22:35 -0400;
14cac48 [FIX] Add ms2_m_score definition, select detecting/identifying transitions before inner join, get precursorInfo in one line with if-else for DIA IPF case by Justin Sing <justincsing@gmail.com> 2021-06-16 18:20:21 -0400;
3fa4c6d [FIX] Changed remaping using purely data.table instead of dplyr in ipfReassignFDR method, added setcolorder to roxygen documentation in getMultipeptide by Justin Sing <justincsing@gmail.com> 2021-06-16 17:30:52 -0400;
d388c33 [FIX] Fix typo in paramsDIAlignR documentation by Justin Sing <justincsing@gmail.com> 2021-06-16 00:35:15 -0400;
ab325af [FEATURE] Add support for IPF PTMs alignment. PTM osw XICs are not added yet. by Justin Sing <justincsing@gmail.com> 2021-06-16 00:17:53 -0400;
263fd09 [Fix] Bioconductor Warning message by Shubham <sgupt46@alumni.uwo.ca> 2021-05-27 13:29:44 -0400;
9967db7 [Fix] Added parameter to select method to build a tree by Shubham <sgupt46@alumni.uwo.ca> 2021-05-24 16:26:36 -0400;
982a9fb Merge branch 'master' of git.bioconductor.org:packages/DIAlignR by Shubham <sgupt46@alumni.uwo.ca> 2021-05-23 11:56:51 -0400;
90f687f [Fix] Using RT correlation to calculate distance matrix by Shubham <sgupt46@alumni.uwo.ca> 2021-05-23 11:25:08 -0400;
dcb88aa minor by Shubham <sgupt46@alumni.uwo.ca> 2021-05-22 13:26:33 -0400;
d3b863e [Fix] distance matrix calculation to build the tree by Shubham <sgupt46@alumni.uwo.ca> 2021-05-22 11:55:34 -0400;
4867e34 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 16:49:08 +0000;
fe5d1ad (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 16:49:08 +0000;
888cbe6 Merge pull request <a href="#14">#14</a> from shubham1637/dev by Shubham Gupta <shubham1637@users.noreply.github.com> 2021-05-19 02:15:38 -0400;
d0984b3 minor by Shubham <sgupt46@alumni.uwo.ca> 2021-05-19 01:24:19 -0400;
e76d739 [Feature] Added MST alignment and other improvements by Shubham <sgupt46@alumni.uwo.ca> 2021-05-17 17:32:34 -0400;
d323ad7 [Fix] Do not stop when star-alignment C++ crashes by Shubham <sgupt46@alumni.uwo.ca> 2021-05-11 08:39:04 -0400;
6d5a117 [BugFix] disconnecting memory database by Shubham <sgupt46@alumni.uwo.ca> 2021-03-13 14:15:11 -0500;
d9e735a [Speed] Fetchinf batch XICs by Shubham <sgupt46@alumni.uwo.ca> 2021-03-13 11:41:19 -0500;
c104eb8 Fixed Bugs by Shubham <sgupt46@alumni.uwo.ca> 2021-03-09 17:32:29 -0500;
fe83967 BugFix by Shubham <sgupt46@alumni.uwo.ca> 2021-03-09 09:42:45 -0500;
9727e2a Bug Fix, max(NA, NA, na.rm = T) by Shubham <sgupt46@alumni.uwo.ca> 2021-03-07 14:50:05 -0500;
673aa7a Bug Fix. Negative time in merged chromatogram no more by Shubham <sgupt46@alumni.uwo.ca> 2021-03-07 10:58:22 -0500;
b00d08a Bug Fix by Shubham <sgupt46@alumni.uwo.ca> 2021-03-06 14:32:08 -0500;
b68787b Bug Fix by Shubham <sgupt46@alumni.uwo.ca> 2021-03-05 18:20:25 -0500;
820be3e Tests +! by Shubham <sgupt46@alumni.uwo.ca> 2021-03-05 07:32:34 -0500;
ca1a45d Bug Fix by Shubham <sgupt46@alumni.uwo.ca> 2021-03-04 14:00:19 -0500;