1. RiboProfiling
  2. Graph
Graph of RiboProfiling
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  • 6466c71 (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 10:45:56 -0400;
  • 8cec7bf (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 10:45:56 -0400;
  • 4837805 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 10:42:20 -0400;
  • 8eb9915 (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 10:42:20 -0400;
  • fadaf0d 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 11:12:25 -0400;
  • 0553477 (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 11:12:25 -0400;
  • 22fa5a9 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 15:27:55 +0000;
  • 9f71470 (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 15:27:55 +0000;
  • c5025aa Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-17 05:50:59 -0800;
  • b52c574 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 16:23:25 +0000;
  • 225f775 (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 16:23:25 +0000;
  • 9542bc6 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 16:16:23 +0000;
  • a315cdd (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 16:16:23 +0000;
  • 616e6ad 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 11:09:02 -0400;
  • 0037574 (origin/RELEASE_3_12, RELEASE_3_12) 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 11:09:02 -0400;
  • a2fd16d 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 18:52:18 +0000;
  • dc54a2a (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 18:52:18 +0000;
  • c6c97fa 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 13:40:06 -0400;
  • eaed267 (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 13:09:29 -0400;
  • cbb0ae0 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 12:13:04 -0400;
  • 1f72e8e (origin/RELEASE_3_9, RELEASE_3_9) bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 11:53:58 -0400;
  • 21d123c bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:35 -0400;
  • edf20ed (origin/RELEASE_3_8, RELEASE_3_8) bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:59 -0400;
  • 2a030ea bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:41 -0400;
  • eac8e47 (origin/RELEASE_3_7, RELEASE_3_7) bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:35:38 -0400;
  • 6d6a1e4 (origin/RELEASE_3_6, RELEASE_3_6) Corrected biocStyle error in author field in the vignette by apopa <alexandra.mariela.popa@gmail.com> 2017-12-13 15:58:53 +0100;
  • 6acc9d8 Corrected biocStyle error in author field in the vignette by apopa <alexandra.mariela.popa@gmail.com> 2017-12-11 14:50:43 +0100;
  • e1444bd bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:54:16 -0400;
  • 7fff2d1 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:41:07 -0400;
  • e25e74e use pruning.mode="coarse" instead of force=TRUE when calling seqlevels() setter by Herve Pages <hpages@fhcrc.org> 2017-04-29 21:19:50 +0000;
  • a679b3d bump x.y.z versions to odd y after creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:50:57 +0000;
  • 03ac91c (origin/RELEASE_3_5, RELEASE_3_5) Creating branch for BioC 3.5 release by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:45:44 +0000;
  • 05af6e8 bump x.y.z versions to even y prior to creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:25:24 +0000;
  • f8dc1ef Corrected a bug in utils.R, readStartCov1Aln function. by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2017-04-05 10:52:29 +0000;
  • 9d89c83 (origin/RELEASE_3_4, RELEASE_3_4) o TIMEOUT BUG fix For the vignette the example bam files have been down-sampled and added to the extdata folder o Down-sampled the ctrlGAlignments.rda object from the data folder o Changed conflicting sweave-knitr in the vignette by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2017-01-19 14:43:14 +0000;
  • ea5c65a - downsamples the ctrlGAlignments.rda object from the data folder - changed conflicting sweave-knitr in the vignette by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2017-01-13 10:27:56 +0000;
  • 210be46 - downsampled the bam files and added them to the extdata instead of downloading them from the server. Changed the vignette accrodingly by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2017-01-11 07:49:26 +0000;
  • 3aef74d bump x.y.z versions to odd 'y' after creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:10:43 +0000;
  • dfb6974 Creating branch for BioC 3.4 release by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:00:47 +0000;
  • 5ff24bd bump x.y.z versions to even 'y' prior to creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 18:45:06 +0000;
  • 154ef5a (origin/RELEASE_3_3, RELEASE_3_3) Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-15 20:18:19 +0000;
  • 0077cde Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-15 20:14:22 +0000;
  • 310f358 Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-11 23:15:25 +0000;
  • a77e824 Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-11 23:05:31 +0000;
  • eefd2ed bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • 6b0d215 Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
  • 7bd7ab3 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • 7388f1b allowed for overlapping codon motifs (from 1 and up to 3 codons) - shifted by 3 nucleotides each time changed codonInfo and countShiftReads accordingly replaced elementLengths by elementNROWS from S4Vectors solved some memory problems for 3 codon motifs in codonInfo by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-26 04:49:47 +0000;
  • e07bc60 (origin/RELEASE_3_2, RELEASE_3_2) o Changed GenomicFeatures::makeTranscriptDbFromUCSC to GenomicFeatures::makeTxDbFromUCSC o In vignette added Rsamtools:: before the BamFile function by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-16 10:14:35 +0000;
  • da52ff1 as.table not exported by IRanges by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-15 14:16:39 +0000;
  • 586b6c1 SummarizedExperiment::assay added parameter paramScanBAM (ScanBamParam object) to riboSeqFromBAM function by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-10 22:14:16 +0000;
  • 9093848 assays from GenomicRanges gave and error as it is no longer exported by this package. -> error corrected by eliminating the GenomicRanges:: call by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-08 09:12:15 +0000;
  • 0983b3c corrected my mistake of the previous commit where I had the wrong version of my corrections by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-03 22:04:44 +0000;
  • 5981a63 added the readToStartOrEnd function by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-03 21:24:36 +0000;
  • ab6c07b --force-log by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-03 21:10:05 +0000;
  • feb2285 --force-log by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2016-02-03 20:58:45 +0000;
  • b1f2fa8 elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon) by Herve Pages <hpages@fhcrc.org> 2016-01-29 01:22:03 +0000;
  • 9a41d6f the ggbio package does not export the ggplot symbol anymore by Herve Pages <hpages@fhcrc.org> 2016-01-29 00:58:38 +0000;
  • 84a4610 the ggbio package does not export the ggplot symbol anymore by Herve Pages <hpages@fhcrc.org> 2016-01-29 00:53:04 +0000;
  • 56efc1c fix imports by Herve Pages <hpages@fhcrc.org> 2015-12-02 21:28:54 +0000;
  • 9841c8c --force-log by Alexandra Popa <alexandra.mariela.popa@gmail.com> 2015-10-29 14:08:45 +0000;
  • c2c8740 Bumped version number of all packages after creation of 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:59:53 +0000;
  • 8b078dd Creating branch for BioC 3.2 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:57:33 +0000;
  • a31d52e Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
  • 414f66f Add DChIPRep, GeneBreak, RiboProfiling, SNPhood by James Hester <jhester@fredhutch.org> 2015-10-07 21:42:50 +0000;