CHANGES IN VERSION 0.15.3 ------------------------- o Working up new API (see issue #41) <2017-04-09 Sun> o Temporarily remove some vignettes, until the API has stabilised. <2017-04-09 Sun> CHANGES IN VERSION 0.15.2 ------------------------- o New Proteins class implementation - see issue #38. <2016-12-10 Sat> o Fixed many errors from current rewrite <2017-04-08 Sat> CHANGES IN VERSION 0.15.1 ------------------------- o Proteins,EnsDb method allowing to fetch a Proteins object from an EnsDb database. o Fixes in the mapToGenome method: - Works also for negative strand encoded proteins (issue #29). - Supports a GRangesList object with arbitrary mcols. - Faster implementation (issue #30). o mapToGenome,Proteins,EnsDb and pmapToGenome,Proteins,EnsDb methods that map peptide features to the genome using annotations fetched from an EnsDb. o The seqnames of the Proteins object are used as names for the resulting GRangesList object from the mapToGenome and pmapToGenome methods (issue #34). CHANGES IN VERSION 0.15.1 ------------------------- o Drop unique `seqnames` requirement; see #28, #32 o Create `names` as synonym for `seqnames`; close #32 CHANGES IN VERSION 0.13.3 ------------------------- o Update mapping vignette index entry, as suggested by Mike Love <2016-09-13 Tue> CHANGES IN VERSION 0.13.0 ------------------------- o Bioc devel CHANGES IN VERSION 0.11.3 ------------------------- o acols and pranges replacement method <2016-02-22 Mon> CHANGES IN VERSION 0.11.2 ------------------------- o add addPeptideFragments; see #24 for details [2016-02-07 Sun] CHANGES IN VERSION 0.11.1 ------------------------- o elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon) [r113044 | hpages@fhcrc.org | 2016-01-29 01:22:03 +0000 (Fri, 29 Jan 2016)] CHANGES IN VERSION 0.11.0 ------------------------- o New Bioc devel version CHANGES IN VERSION 0.10.0 ------------------------- o New Bioc release version CHANGES IN VERSION 0.9.1 ------------------------ o update cleave method to address build error [2015-10-13 Tue] CHANGES IN VERSION 0.9.0 ------------------------ o Bioc devel 3.2 CHANGES IN VERSION 0.8.0 ------------------------ o Bioc release 3.1 CHANGES IN VERSION 0.6.13 ------------------------- o Updating Biomart query to reflect changes [2015-04-06 Mon] CHANGES IN VERSION 0.6.12 ------------------------- o Fix filling in tracks plots [2015-03-07 Sat] CHANGES IN VERSION 0.6.11 ------------------------- o Documentation for the plotting heler functions [2015-02-28 Sat] CHANGES IN VERSION 0.6.10 ------------------------- o plotting helper functions [2015-02-28 Sat] o fixed peptide grouping [2015-02-28 Sat] CHANGES IN VERSION 0.6.9 ------------------------ o Fixing junction peptides splitting to support peptides reaching > 2 exons [2015-02-27 Fri] o supporting more protein coding biotypes [2015-02-27 Fri] o rewrite and simplify proteinCoverage; closes #19 [2015-02-27 Fri] CHANGES IN VERSION 0.6.8 ------------------------ o fix splitting exon junction ranges [2015-02-26 Thu] CHANGES IN VERSION 0.6.7 ------------------------ o The genomic coordinates of peptides that overlap exon junctions are now correctly split instead of spanning over the exon and are grouped accordingly. [2015-02-26 Thu] CHANGES IN VERSION 0.6.6 ------------------------ o update mapping vignette and use alignment to identify correct transcript [2015-02-25 Wed] CHANGES IN VERSION 0.6.5 ------------------------ o see also mapping vignette in ?mapToGenome [2015-02-20 Fri] o calculateHeavyLabels, isCleaved, proteotypic and proteinCoverage are is now a function [2015-02-20 Fri] o added accessors to Pbase:::pplot() and update Pbase-data vignette accordingly [2015-02-21 Sat] CHANGES IN VERSION 0.6.4 ------------------------ o typos in man [2015-02-19 Thu] o Added use.names argument ot etrid2gel [2015-02-19 Thu] o mapToGenome,Proteins,GRangesList (remove GRanges) using names for 1-to-many mapping and document in mapping vignette [2015-02-19 Thu] CHANGES IN VERSION 0.6.3 ------------------------ o new fig in Pbase-data vignette [2015-02-14 Sat] o new section for pmapToGenome in mapping vignette [2015-02-14 Sat] CHANGES IN VERSION 0.6.2 ------------------------ o Add uniprot release to p metadata [2015-02-14 Sat] o added a metadata update method [2015-02-14 Sat] CHANGES IN VERSION 0.6.1 ------------------------ o [p]mapToGenome methods [2015-02-14 Sat] CHANGES IN VERSION 0.6.0 ------------------------ o fixed typos in vigs [2015-02-12 Thu] o new etrid2grl function to convert Ensembl transcript identifiers to GRangesList objects [2015-02-13 Fri] o initial mapToGenome function [2015-02-13 Fri] o regenerated p data using latest UniProt release and added acols(p)$ENST [2015-02-13 Fri] CHANGES IN VERSION 0.5.5 ------------------------ o various fixes in vignettes [2015-02-12 Thu] CHANGES IN VERSION 0.5.4 ------------------------ o Ensembl - UCSC mapping vignette [2015-02-11 Wed] CHANGES IN VERSION 0.5.3 ------------------------ o Render vignettes with rmarkdown [2015-02-11 Wed] o Improve mapping vignette [2015-02-11 Wed] CHANGES IN VERSION 0.5.2 ------------------------ o Adapt to new `addIdentification` signature in MSnbase >= 1.15.5. [2015-02-10 Tue] CHANGES IN VERSION 0.5.1 ------------------------ o Update vignette since TxDb's UCSC coordinates differ from those fetched from Ensembl via biomaRt. [2015-01-05 Mon] o Add `isCleaved` method. [2015-01-03 Sat] o Add `calculateHeavyLabels`; closes #6 and cleaver#5. [2015-01-03 Sat] CHANGES IN VERSION 0.5.0 ------------------------ o Bump version for new Bioc release. CHANGES IN VERSION 0.2.2 ------------------------ o Fix warning re undocumented '[' and siglist 'Proteins,ANY,ANY,ANY' [2014-10-03 Fri] CHANGES IN VERSION 0.2.1 ------------------------ o Counting id files when adding [2014-09-17 Wed] CHANGES IN VERSION 0.2.0 ------------------------ o support for mzID and mzR (new) to extract identification data from mzid files via addIdentificationData [2014-09-12 Fri] o support to add id data from > 1 mzid file [2014-09-12 Fri] o new Pparams parameter infrastructure [2014-09-13 Sat] CHANGES IN VERSION 0.1.10 ------------------------- o Allow spaces in GeneNames (GN) of fasta comments; fixes #7 [2014-09-13 Sat] CHANGES IN VERSION 0.1.9 ------------------------ o Use BioStyle CHANGES IN VERSION 0.1.8 ------------------------ o Using knit2html instead of rmarkdown::render since it is not yet available on the Bioc build servers [2014-07-24 Thu] CHANGES IN VERSION 0.1.7 ------------------------ o export vignettes [2014-07-22 Tue] CHANGES IN VERSION 0.1.6 ------------------------ o New mapping vignette [2014-07-17 Thu] o Raw MSMS data pms data [2014-07-17 Thu] CHANGES IN VERSION 0.1.5 ------------------------ o new data object p and vignette [2014-07-15 Tue] CHANGES IN VERSION 0.1.4 ------------------------ o Fixed issues with proteins without any identifications in addIdentification Data; see also rmEmptyRanges functions to remove such proteins [2014-07-14 Mon] CHANGES IN VERSION 0.1.1 ------------------------ o add biocViews and update README [2014-06-09 Mon] CHANGES IN VERSION 0.1.0 ------------------------ o Added basic Proteins class [2014-05-02 Fri]