1. PhIPData
  2. Graph
Graph of PhIPData
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  • 7b83585 (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 11:30:33 -0400;
  • 463fdc6 (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 11:30:33 -0400;
  • 57d6470 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 11:27:16 -0400;
  • a9ab936 (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 11:27:16 -0400;
  • 076c043 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 11:24:09 -0400;
  • 0b4522b (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 11:24:09 -0400;
  • 030493e 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 16:13:30 +0000;
  • 1da367a (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 16:13:30 +0000;
  • 2368993 Bumped version by Athena Chen <achen70@jhu.edu> 2022-02-04 21:39:37 -0500;
  • 94589e6 changed to BiocFileCache by Athena Chen <achen70@jhu.edu> 2022-02-04 21:12:15 -0500;
  • e4e5956 updated gh actions by Athena Chen <achen70@jhu.edu> 2022-02-04 12:05:55 -0500;
  • 8c35a3c fixed more file.path problems hopefully, deleted exd executable for bioc check by Athena Chen <achen70@jhu.edu> 2022-02-04 11:28:41 -0500;
  • 04cad86 updated news format and BioCchek by Athena Chen <achen70@jhu.edu> 2022-02-03 14:48:03 -0500;
  • 1e6f3bd updated paths by Athena Chen <achen70@jhu.edu> 2022-02-03 14:01:49 -0500;
  • 7cc729d changed path code by Athena Chen <achen70@jhu.edu> 2022-02-02 09:13:19 -0500;
  • d958c8b Merge remote-tracking branch 'upstream/master' by Athena Chen <achen70@jhu.edu> 2022-02-02 09:10:59 -0500;
  • aafabf9 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 17:07:31 +0000;
  • 4e37055 (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 17:07:31 +0000;
  • 0691dee corrected typo in error msg by Athena Chen <achen70@jhu.edu> 2021-08-26 14:18:58 -0400;
  • 7a1a190 bumped version number by Athena Chen <achen70@jhu.edu> 2021-08-23 12:02:56 -0400;
  • 7e203a9 Removed unnecessary tests by Athena Chen <achen70@jhu.edu> 2021-08-23 11:45:43 -0400;
  • acb7761 Added dependence for tests by Athena Chen <achen70@jhu.edu> 2021-08-19 16:47:52 -0500;
  • c6a0335 Modified RCMD check by Athena Chen <achen70@jhu.edu> 2021-08-19 16:27:28 -0500;
  • 4bb4bec Corrected bug in onLoad that did not make assignments to pkg environment by Athena Chen <achen70@jhu.edu> 2021-08-19 15:04:32 -0500;
  • 85fc287 Added .onLoad to build and update defaults as necessary by Athena Chen <achen70@jhu.edu> 2021-08-19 14:45:40 -0500;
  • c4b684b Added defaults to .gitignore so that user-specific profiles are rebuilt by Athena Chen <achen70@jhu.edu> 2021-08-19 14:44:21 -0500;
  • f8da901 Changed from global env variables to package environment variables for storing alias, library, beads-only indicators by Athena Chen <achen70@jhu.edu> 2021-08-19 13:46:21 -0500;
  • a53a14b Added changes to NEWS.md by Athena Chen <achen70@jhu.edu> 2021-08-18 16:20:31 -0500;
  • 66947a6 Added coercion function to convert a PhIPData object to a DataFrame by Athena Chen <achen70@jhu.edu> 2021-08-18 16:09:36 -0500;
  • 897c60d bumped version by Athena Chen <achen70@jhu.edu> 2021-08-05 19:15:14 -0500;
  • 68b3327 Standardized code style by Athena Chen <achen70@jhu.edu> 2021-08-05 17:45:47 -0500;
  • 89c8c30 Updated documentation for propReads file and updated badges on README to include Bioc badge by Athena Chen <achen70@jhu.edu> 2021-08-05 17:20:51 -0500;
  • ab4c013 Added function to calculate proportion of reads by Athena Chen <achen70@jhu.edu> 2021-08-05 16:46:02 -0500;
  • 8aea0b1 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 17:00:28 +0000;
  • 988e473 (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 17:00:28 +0000;
  • ed6cff0 bumped version to trigger Bioconductor build by Athena Chen <achen70@jhu.edu> 2021-03-17 18:08:23 -0400;
  • 66bb97c Renamed `scripts` folder to `script` by Athena Chen <achen70@jhu.edu> 2021-03-17 17:39:15 -0400;
  • 388dafc Added inst/scripts/ for inst/extdata description, updated some of the line widths by Athena Chen <achen70@jhu.edu> 2021-03-17 17:26:24 -0400;
  • 66c27a4 bumped R requirement by Athena Chen <achen70@jhu.edu> 2021-03-02 10:00:31 -0500;
  • c5d55b2 Removed .Rproj file by Athena Chen <achen70@jhu.edu> 2021-03-02 09:44:32 -0500;
  • 7af3909 Fixed NEWS formatting by Athena Chen <achen70@jhu.edu> 2021-03-01 10:43:54 -0500;
  • a0969ea Store assays as matrices rather than DataFrames by Athena Chen <achen70@jhu.edu> 2021-02-18 11:28:36 -0500;
  • ac7a6b8 Corrected news formatting by Athena Chen <achen70@jhu.edu> 2021-02-17 10:03:49 -0500;
  • 5b2faad Fixed BiocCheck warnings by Athena Chen <achen70@jhu.edu> 2021-02-16 15:08:34 -0500;
  • fcfe4b6 Added message indicating that while counts are normally integers, non-integer values can be stored in counts. by Athena Chen <achen70@jhu.edu> 2021-02-15 12:09:11 -0500;
  • 6538269 * Updated version to be compatible with Bioc submission guidelines. * Added librarySize + subsetBeads example to vignette by Athena Chen <achen70@jhu.edu> 2021-02-15 11:59:09 -0500;
  • 23f14eb Add NEWS.md by Athena Chen <achen70@jhu.edu> 2021-02-15 11:06:18 -0500;
  • aef9d27 Added functions to subset beads-only and to calculate library sizes. by Athena Chen <achen70@jhu.edu> 2021-02-12 00:23:16 -0500;
  • c40196d Vectorized alias functions by Athena Chen <achen70@jhu.edu> 2021-02-11 18:42:06 -0500;
  • b5d0bdc 7th time is the charm? by Athena Chen <achen70@jhu.edu> 2021-02-10 21:07:20 -0500;
  • 71a8e0f R6 by Athena Chen <achen70@jhu.edu> 2021-02-10 20:59:28 -0500;
  • 49c7b00 R5 by Athena Chen <achen70@jhu.edu> 2021-02-10 20:39:49 -0500;
  • a149024 Round 4 by Athena Chen <achen70@jhu.edu> 2021-02-10 20:28:13 -0500;
  • ad69756 Round 3 on fixing windows bug by Athena Chen <achen70@jhu.edu> 2021-02-10 20:15:24 -0500;
  • e06efd3 testing is_windows function; will break linux/mac tests by Athena Chen <achen70@jhu.edu> 2021-02-10 20:04:03 -0500;
  • 221a035 Windows tests attempt <a href="#2">#2</a> by Athena Chen <achen70@jhu.edu> 2021-02-10 19:46:03 -0500;
  • 0bc4475 Made the Library path tests windows compatible by Athena Chen <achen70@jhu.edu> 2021-02-10 19:33:02 -0500;
  • a773be2 updated bioc workflow to match current bioc version by Athena Chen <achen70@jhu.edu> 2021-02-10 18:58:00 -0500;
  • 81ea2d1 Added documentation, should pass R CMD checks by Athena Chen <achen70@jhu.edu> 2021-02-10 18:00:50 -0500;
  • b7b1c36 Added documentation, updated README by Athena Chen <achen70@jhu.edu> 2021-02-04 19:48:44 -0500;
  • d0bc6ac Modified constructor: - Counts are stored as non-negative integers, if coercion truncated the data, an error is returned. - `group` column to store beads-only indicator is added if the column is not present. If no beads-only samples are present, print a warning. Modified validity: - Counts have to be integers - `group` must be included in the sampleInfo Show function: - Added entry that shows the # of beads only samples and what is used as reference to the beads-only by Athena Chen <achen70@jhu.edu> 2021-02-01 13:27:01 -0500;
  • 8df151f removed subsetByPeptideMeta() since subset() does the same thing by Athena Chen <achen70@jhu.edu> 2021-01-21 21:40:53 -0500;
  • b23739d completed vignette by Athena Chen <achen70@jhu.edu> 2021-01-21 14:51:50 -0500;
  • f074253 increased code coverage by Athena Chen <achen70@jhu.edu> 2021-01-18 18:01:26 -0500;
  • c1768d7 increased code coverage by Athena Chen <achen70@jhu.edu> 2021-01-18 18:01:10 -0500;
  • f7d069f modified subsetByPeptides function to be more general by Athena Chen <achen70@jhu.edu> 2021-01-18 17:37:32 -0500;
  • 29948da modified PhIPData class to be able to add/replace/remove assays with tidy names by Athena Chen <achen70@jhu.edu> 2021-01-17 15:40:28 -0500;
  • 24788ee - Made alias error messages more consistent - Added tests by Athena Chen <achen70@jhu.edu> 2021-01-06 18:29:13 -0500;
  • 235eab7 Updated setAlias and deleteAlias functions to work with alias.rda in extdata folder; use new environment to ensure continuity by Athena Chen <achen70@jhu.edu> 2021-01-06 17:46:03 -0500;
  • c9f65ac corrected "inst" typo in library specification by Athena Chen <achen70@jhu.edu> 2021-01-06 16:22:34 -0500;
  • b8600e4 Modified test to clean up after itself by Athena Chen <achen70@jhu.edu> 2021-01-06 16:07:00 -0500;
  • cd8eafc Added virscan example to library folder (so that it pushes to github) by Athena Chen <achen70@jhu.edu> 2021-01-06 16:05:51 -0500;
  • d1a7d03 - changed global variable name from LIBRARY_PATH to PHIP_LIBRARY_PATH To avoid conflicts on the cluster - added menu for user to select to overwrite/not overwrite library file if it already exists by Athena Chen <achen70@jhu.edu> 2021-01-06 16:05:22 -0500;
  • 0eb3cf3 testing to see if this works on the cluster by Athena Chen <achen70@jhu.edu> 2021-01-06 15:27:28 -0500;
  • 9bfe278 Edited alias function to use extdata folder by Athena Chen <achen70@jhu.edu> 2021-01-06 15:06:39 -0500;
  • 34b186a testing to see if data dir can be directly accessed by Athena Chen <achen70@jhu.edu> 2021-01-06 14:45:47 -0500;
  • f9c4910 updated namespace by Athena Chen <achen70@jhu.edu> 2021-01-06 14:40:30 -0500;
  • b0b28d4 added export indicators by Athena Chen <achen70@jhu.edu> 2021-01-06 14:37:17 -0500;
  • 8360313 edited path for alias by Athena Chen <achen70@jhu.edu> 2021-01-06 14:20:40 -0500;
  • 5d56adb added bioc and coverage workflows for ghactions by Athena Chen <achen70@jhu.edu> 2021-01-06 13:30:52 -0500;
  • 63970b8 - Renamed species/genus columns in virscan data - Updated tests to use data in inst/extdata by Athena Chen <achen70@jhu.edu> 2021-01-06 13:08:24 -0500;
  • d800a5c - Added mini-virscan for test example - Modified library to point to inst folder by default. by Athena Chen <achen70@jhu.edu> 2021-01-06 12:26:33 -0500;
  • 74817dc Renamed getPeptides to subsetPeptides by Athena Chen <achen70@jhu.edu> 2021-01-06 11:32:29 -0500;
  • 8c9387f * Added code coverage * changed README to be generated by RmD * Added vignette template by Athena Chen <achen70@jhu.edu> 2021-01-06 11:31:04 -0500;
  • 50dd26b added library creators ad tests by Athena Chen <achen70@jhu.edu> 2021-01-04 20:08:45 -0500;
  • 00e61e1 added updated Description and README by Athena Chen <achen70@jhu.edu> 2021-01-04 15:51:45 -0500;
  • 2a5d44f added CLI output, added peptide filter and library filter by Athena Chen <achen70@jhu.edu> 2021-01-04 15:50:33 -0500;
  • f12dd66 Constructor finally passes all validity checks, all sample name checks, and all functioning checks. Added tests to verify that they worked, corrected typos in the getSample/PeptideNames function, added workaround where dimension names of DataFrame cannot be set to empty by Athena Chen <achen70@jhu.edu> 2020-12-03 16:15:19 -0500;
  • 5344a7d verified that getters and validity methods work as desired by Athena Chen <achen70@jhu.edu> 2020-12-02 22:42:54 -0500;
  • d10f79d updated to-do list by Athena Chen <achen70@jhu.edu> 2020-12-02 00:51:30 -0500;
  • a356af4 added setters for assays, still need to make setters for annotations and names by Athena Chen <achen70@jhu.edu> 2020-12-02 00:48:37 -0500;
  • fd210d3 added validity, still need to test by Athena Chen <achen70@jhu.edu> 2020-12-02 00:44:17 -0500;
  • 7e5638b modularized constructor by Athena Chen <achen70@jhu.edu> 2020-12-02 00:40:16 -0500;
  • 3001eb8 added validity method and basic getters by Athena Chen <achen70@jhu.edu> 2020-12-01 18:36:18 -0500;
  • c5af2a7 completed constructor so that it will coerce to matrices/df to DataFrames by Athena Chen <achen70@jhu.edu> 2020-11-30 19:25:17 -0500;
  • 6f9951f working constructor added, currently only accepts matrices, need initial coersion to DataFrames by Athena Chen <achen70@jhu.edu> 2020-11-30 16:50:54 -0500;
  • 133587f Removed files extra Rstudio files by Athena Chen <achen70@jhu.edu> 2020-11-30 16:46:35 -0500;
  • b3b039e Removed files extra Rstudio files by Athena Chen <achen70@jhu.edu> 2020-11-30 16:46:02 -0500;
  • 2a6c394 modified .gitignore to ignore rstudio files by Athena Chen <achen70@jhu.edu> 2020-11-30 16:43:33 -0500;
  • 9d94988 added README by Athena Chen <achen70@jhu.edu> 2020-11-21 14:53:37 -0500;