RELEASE HISTORY OF THE "cleaver" PACKAGE ======================================== Version 1.41.3 [2024-04-24]: - Add 3 different types of trypsin (as defined in PeptideMass): trypsin-high (identical to the current trypsin rule and to PeptideMass' "higher specificity"), trypsin-low (cleavage after K/R but not if followed by P), trypsin-simple (cleavage after K/R even if followed by P); The trypsin rule is identical to trypsin-high and will be kept for backward compatibility. Version 1.41.2 [2023-12-03]: - Add missing documentation for LysargiNase. Version 1.41.1 [2023-11-30]: - Add LysargiNase cleavage rule. Version 1.35.1 [2022-08-31]: - Fix: adapt vignette code to new UniProt.ws. Version 1.27.1 [2020-06-05]: - Fix cleavage rule for glutamyl endopeptidase in documentation Thanks to Mariia Chernigovskaya for reporting this error. Version 1.25.1 [2019-12-30]: - Add missing space in vignette. Version 1.21.4 [2018-12-26]: - Use "https" in hyperlinks (where possible). Version 1.21.3 [2018-12-26]: - Correct cleavage rules for "pepsin" and "pepsin1.3". According to the peptidecutter documentation "pepsin1.3" is more specific (cleaves at [FL]) than "pepsin" (cleaves [FLWY]); see https://github.com/sgibb/cleaver/issues/6 for details. Thanks to Jean Manguy for reporting this error. Version 1.21.2 [2018-11-03]: - Convert vignette from Sweave to rmarkdown. - Another try to fix links in manual pages to avoid WARNING on Windows. Version 1.21.1 [2018-11-01]: - Add my ORCID to the Author field in DESCRIPTION. - Fix links in manual pages to avoid WARNING on Windows. Version 1.15.1 [2017-06-08]: - Don't consider the last aminoacid as cleavage site. `cleavageSites("ACK", custom="K")` results in `integer()` instead of `3` now. Thanks Apurva Hegde for reporting this issue. - Remove superfluous "missedCleavages" argument in `cleavageSites`. Version 1.13.2 [2017-02-14]: - Use `expect_equal` instead of `expect_identical` to avoid failing of the `.revsequence` unit test on "toluca2" (Mac OS X Mavericks (10.9.5) / x86_64). - Add "importFrom(stats, setNames)" to NAMESPACE. Version 1.13.1 [2017-01-04]: - Remove GPL headers from *.R files. - Remove useless return calls. Version 1.5.3 [2015-02-02]: - Set taxId=9606 for UniProt.ws in vignette. Version 1.5.1 [2015-01-24]: - Add test case if number of cleavage sites is smaller than the number of allowed missed cleavages. Version 1.3.8 [2014-09-28]: - Use title case in the "Title:" field of the DESCRIPTION file. Version 1.3.7 [2014-05-08]: - Create an IRangesList using `split` instead of `lapply` in the cleavageRanges,AAStringSet-method is more than two times faster. Version 1.3.6 [2014-05-03]: - Add cleavageRanges method for character, AAString and AAStringSet. - cleave,AAString returns an AAStringSet instead of an AAStringSetList object. - Fix return value of cleavageSites,AAStringSet. Version 1.3.5 [2014-04-30]: - Fix defintion of cleavageSites,AAStringSet. Version 1.3.4 [2014-04-30]: - Add cleavageSites method for character, AAString and AAStringSet. Version 1.3.3 [2014-04-28]: - Avoid duplicated digest of peptides results in a hugh speed improvement and a hugh memory reduction (removes fix from 1.1.8 and partly reintroduces original algorithm). - Remove memory test and "memoryThreshold" argument (fails on different platforms and is not important anymore using the "new" cleavage algorithm). - Change default of "unique" argument to "unique=TRUE". Version 1.3.2 [2014-04-25]: - Introduce simple memory test and "memoryThreshold" argument to avoid the calculation of ridiculous high numbers of "missedCleavages" and peptide combinations. Version 1.3.1 [2014-04-25]: - Add "custom" argument to allow the user defining own cleavage rules. Version 1.1.8 [2014-03-26]: - Fix missedCleavages>1. - Add argument "unique". - Add methods, Biostrings, IRanges to NAMESPACE. Version 1.1.7 [2014-03-25]: - Typo in the manual page. Version 1.1.5 [2014-02-25]: - Using AAStringSetList constructor for list of characters instead of creating a lot of AAStringSets dramatically decreases running time for cleave,AAStringSet-method. Version 1.1.4 [2013-12-20]: - tests: - move tests into tests/testthat to adapt to testthat 0.8 and new CRAN policy. Version 0.99.5 [2013-07-24]: - vignette: - remove duplicated sessionInfo entries. Version 0.99.4 [2013-07-23]: - vignette: - use BiocStyle. - add sessionInfo() and TOC. Version 0.99.3 [2013-07-08]: - vignette: add second BRAIN reference. Version 0.99.2 [2013-06-17]: - Replace own AAStringSetList constructor by Biostrings::AAStringSetList. - man/cleaver-package.Rd: remove static date. - vignette: add dynamic date and don't load Biostrings manually anymore. - NAMESPACE: don't import from Biostrings and IRanges. Version 0.99.1 [2013-05-30]: - Add S4-methods for character, AAString, AAStringSet. - man/cleave-methods.Rd: split table of cleavage rules to reduce table width. - Extend vignette (add BRAIN and UniProt.ws based examples). Version 0.99.0 [2013-04-27]: - Initial release.