NEWS

---

cleaver 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.

cleaver 1.41.2 (2023-12-03)

• Add missing documentation for LysargiNase.

cleaver 1.41.1 (2023-11-30)

• Add LysargiNase cleavage rule.

cleaver 1.35.1 (2022-08-31)

• Fix: adapt vignette code to new UniProt.ws.

cleaver 1.27.1 (2020-06-05)

• Fix cleavage rule for glutamyl endopeptidase in documentation Thanks to Mariia Chernigovskaya <[email protected]> for reporting this error.

cleaver 1.25.1 (2019-12-30)

• Add missing space in vignette.

cleaver 1.21.4 (2018-12-26)

• Use "https" in hyperlinks (where possible).

cleaver 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 <[email protected]> for reporting this error.

cleaver 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.

cleaver 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.

cleaver 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 <[email protected]> for reporting this issue.
• Remove superfluous "missedCleavages" argument in 'cleavageSites'.

cleaver 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.

cleaver 1.13.1 (2017-01-04)

• Remove GPL headers from *.R files.
• Remove useless return calls.

cleaver 1.5.3 (2015-02-02)

• Set taxId=9606 for UniProt.ws in vignette.

cleaver 1.5.1 (2015-01-24)

• Add test case if number of cleavage sites is smaller than the number of allowed missed cleavages.

cleaver 1.3.8 (2014-09-28)

• Use title case in the "Title:" field of the DESCRIPTION file.

cleaver 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.

cleaver 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.

cleaver 1.3.5 (2014-04-30)

• Fix defintion of cleavageSites,AAStringSet.

cleaver 1.3.4 (2014-04-30)

• Add cleavageSites method for character, AAString and AAStringSet.

cleaver 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".

cleaver 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.

cleaver 1.3.1 (2014-04-25)

• Add "custom" argument to allow the user defining own cleavage rules.

cleaver 1.1.8 (2014-03-26)

• Fix missedCleavages>1.
• Add argument "unique".
• Add methods, Biostrings, IRanges to NAMESPACE.

cleaver 1.1.7 (2014-03-25)

• Typo in the manual page.

cleaver 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.

cleaver 1.1.4 (2013-12-20)

• tests:
• move tests into tests/testthat to adapt to testthat 0.8 and new CRAN policy.

cleaver 0.99.5 (2013-07-24)

• vignette:
• remove duplicated sessionInfo entries.

cleaver 0.99.4 (2013-07-23)

• vignette:
• use BiocStyle.
• add sessionInfo() and TOC.

cleaver 0.99.3 (2013-07-08)

• vignette: add second BRAIN reference.

cleaver 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.

cleaver 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).

cleaver 0.99.0 (2013-04-27)

• Initial release.