Changes in version 1.47.1 (2025-10-14) o Move package to codeberg.org. Changes in version 1.41.3 (2024-04-24) o 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. Changes in version 1.41.2 (2023-12-03) o Add missing documentation for LysargiNase. Changes in version 1.41.1 (2023-11-30) o Add LysargiNase cleavage rule. Changes in version 1.35.1 (2022-08-31) o Fix: adapt vignette code to new UniProt.ws. Changes in version 1.27.1 (2020-06-05) o Fix cleavage rule for glutamyl endopeptidase in documentation Thanks to Mariia Chernigovskaya for reporting this error. Changes in version 1.25.1 (2019-12-30) o Add missing space in vignette. Changes in version 1.21.4 (2018-12-26) o Use "https" in hyperlinks (where possible). Changes in version 1.21.3 (2018-12-26) o 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://codeberg.org/sgibb/cleaver/issues/6 for details. Thanks to Jean Manguy for reporting this error. Changes in version 1.21.2 (2018-11-03) o Convert vignette from Sweave to rmarkdown. o Another try to fix links in manual pages to avoid WARNING on Windows. Changes in version 1.21.1 (2018-11-01) o Add my ORCID to the Author field in DESCRIPTION. o Fix links in manual pages to avoid WARNING on Windows. Changes in version 1.15.1 (2017-06-08) o 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. o Remove superfluous "missedCleavages" argument in `cleavageSites`. Changes in version 1.13.2 (2017-02-14) o 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). o Add "importFrom(stats, setNames)" to NAMESPACE. Changes in version 1.13.1 (2017-01-04) o Remove GPL headers from *.R files. o Remove useless return calls. Changes in version 1.5.3 (2015-02-02) o Set taxId=9606 for UniProt.ws in vignette. Changes in version 1.5.1 (2015-01-24) o Add test case if number of cleavage sites is smaller than the number of allowed missed cleavages. Changes in version 1.3.8 (2014-09-28) o Use title case in the "Title:" field of the DESCRIPTION file. Changes in version 1.3.7 (2014-05-08) o Create an IRangesList using `split` instead of `lapply` in the cleavageRanges,AAStringSet-method is more than two times faster. Changes in version 1.3.6 (2014-05-03) o Add cleavageRanges method for character, AAString and AAStringSet. o cleave,AAString returns an AAStringSet instead of an AAStringSetList object. o Fix return value of cleavageSites,AAStringSet. Changes in version 1.3.5 (2014-04-30) o Fix defintion of cleavageSites,AAStringSet. Changes in version 1.3.4 (2014-04-30) o Add cleavageSites method for character, AAString and AAStringSet. Changes in version 1.3.3 (2014-04-28) o 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). o Remove memory test and "memoryThreshold" argument (fails on different platforms and is not important anymore using the "new" cleavage algorithm). o Change default of "unique" argument to "unique=TRUE". Changes in version 1.3.2 (2014-04-25) o Introduce simple memory test and "memoryThreshold" argument to avoid the calculation of ridiculous high numbers of "missedCleavages" and peptide combinations. Changes in version 1.3.1 (2014-04-25) o Add "custom" argument to allow the user defining own cleavage rules. Changes in version 1.1.8 (2014-03-26) o Fix missedCleavages>1. o Add argument "unique". o Add methods, Biostrings, IRanges to NAMESPACE. Changes in version 1.1.7 (2014-03-25) o Typo in the manual page. Changes in version 1.1.5 (2014-02-25) o Using AAStringSetList constructor for list of characters instead of creating a lot of AAStringSets dramatically decreases running time for cleave,AAStringSet-method. Changes in version 1.1.4 (2013-12-20) o tests: o move tests into tests/testthat to adapt to testthat 0.8 and new CRAN policy. Changes in version 0.99.5 (2013-07-24) o vignette: o remove duplicated sessionInfo entries. Changes in version 0.99.4 (2013-07-23) o vignette: o use BiocStyle. o add sessionInfo() and TOC. Changes in version 0.99.3 (2013-07-08) o vignette: add second BRAIN reference. Changes in version 0.99.2 (2013-06-17) o Replace own AAStringSetList constructor by Biostrings::AAStringSetList. o man/cleaver-package.Rd: remove static date. o vignette: add dynamic date and don't load Biostrings manually anymore. o NAMESPACE: don't import from Biostrings and IRanges. Changes in version 0.99.1 (2013-05-30) o Add S4-methods for character, AAString, AAStringSet. o man/cleave-methods.Rd: split table of cleavage rules to reduce table width. o Extend vignette (add BRAIN and UniProt.ws based examples). Changes in version 0.99.0 (2013-04-27) o Initial release.