CHANGES IN VERSION 1.9.4 ------------------------ o Fix typo <2016-03-01 Tue> CHANGES IN VERSION 1.9.3 ------------------------ o updated msDataTab CHANGES IN VERSION 1.9.2 ------------------------ o more edits to vignette <2015-12-01 Tue> o added Vlas's comprehensive real-life example to the vignette <2015-12-05 Sat> o update msDataTab <2015-12-05 Sat> CHANGES IN VERSION 1.9.1 ------------------------ o updated RforProteomics vignette <2015-11-30 Mon> o (unexported) msDataTable function to create a MS/prot data/objects table <2015-11-30 Mon> o add a short section for readMSnSet[2] <2015-12-01 Tue> CHANGES IN VERSION 1.7.2 ------------------------ o Fix vignette for mzTab v0.9 <2015-09-30 Wed> CHANGES IN VERSION 1.7.1 ------------------------ o Added ReproducibleResearch biocView <2015-06-08 Mon> o Update to MALDIquant 1.12 <2015-06-12 Fri> CHANGES IN VERSION 1.7.0 ------------------------ o Bioc 3.2 devel CHANGES IN VERSION 1.6.0 ------------------------ o Bioc 3.1 release CHANGES IN VERSION 1.5.9 ------------------------ o recompile r4p vignette and add ref to vis vignette [2015-03-23 Mon] o make RProtVis static due to hangs [2015-03-24 Tue] CHANGES IN VERSION 1.5.8 ------------------------ o Vignette updates: simple R plots [2015-02-21 Sat] CHANGES IN VERSION 1.5.7 ------------------------ o suggest rmarkdown (used to render vis vignette) [2015-02-12 Thu] CHANGES IN VERSION 1.5.6 ------------------------ o don't require GNU make [2015-02-11 Wed] CHANGES IN VERSION 1.5.5 ------------------------ o more vis vig updates [2015-01-28 Wed] o added MS animations [2015-01-29 Thu] o document workflows [2015-01-30 Fri] CHANGES IN VERSION 1.5.4 ------------------------ o rename ProtViz() to RProtVis/RProtViz to avoid confusion with the vignette name [2015-01-28 Wed] o RProtVis vignette updates [2015-01-27 Tue] o Use markdown::render [2015-01-27 Tue] CHANGES IN VERSION 1.5.3 ------------------------ o Bioc release version bump CHANGES IN VERSION 1.5.2 ------------------------ o cache package info [2014-11-15 Sat] CHANGES IN VERSION 1.5.1 ------------------------ o update vignette and fixing errors [2014-10-31 Fri] CHANGES IN VERSION 1.5.0 ------------------------ o new devel version for Bioc 3.1 CHANGES IN VERSION 1.4.0 ------------------------ o new release version for Bioc 3.0 CHANGES IN VERSION 1.3.8 ------------------------ o remove github link to MSGFgui since it has now been accepted [2014-10-03 Fri] o new MSnID section [2014-10-04 Sat] CHANGES IN VERSION 1.3.7 ------------------------ o mzR ident section [2014-10-01 Wed] o HUPO2014 poster [2014-10-02 Thu] CHANGES IN VERSION 1.3.6 ------------------------ o new MSGF+/gui sections contributed by Thomas [2014-10-01 Wed] CHANGES IN VERSION 1.3.5 ------------------------ o Proteomics workflow (from Bioc2014 workshop) [2014-08-17 Sun] o Mention viz vig requires Bioc >= 3.0 and link to on-line version [2014-08-27 Wed] o Link to shiyapps/shinyMA [2014-09-03 Wed] o added QC section [2014-10-01 Wed] CHANGES IN VERSION 1.3.4 ------------------------ o Using BiocStyle [2014-08-16 Sat] CHANGES IN VERSION 1.3.3 ------------------------ o Many more sections to RProtVis vignette [2014-08-13 Wed] CHANGES IN VERSION 1.3.2 ------------------------ o RforProteomics wiki on github [2014-08-02 Sat] o Proteomics viz vignette [2014-08-06 Wed] o shinyMA function [2014-08-07 Thu] o fix PXD000001 PRIDE urls [2014-08-08 Fri] o add protViz CRAN package to vig [2014-08-09 Sat] o RProtVis vignette needs MALDIquant >= 1.11 now [2014-08-11 Mon] CHANGES IN VERSION 1.3.1 ------------------------ o get biocView packages as a function [2014-07-23 Wed] o various typos and updates in vignette [2014-07-23 Wed] o functions to get packages for a biocView [2014-07-23 Wed] o relying on cache to reduce build time [2014-07-24 Thu] CHANGES IN VERSION 1.0.18 ------------------------- o pxr renamed rpx [2014-03-28] CHANGES IN VERSION 1.0.17 ------------------------- o using pxr to download data from the PX repository [2014-03-24 Mon] CHANGES IN VERSION 1.0.16 ------------------------- o new downloadData and getThermoHelaPRTC functions [2013-12-14 Sat] CHANGES IN VERSION 1.0.13 ------------------------- o Updates in the MALDIquant section <2013-09-08 Sun> o Fixed new warnings in vignette: cols - columns <2013-09-18 Wed> o do not cache package listing code <2013-09-19 Thu> CHANGES IN VERSION 1.0.12 ------------------------- o Moving cleaver to enhances to all building on Bioc release <2013-07-19 Fri> CHANGES IN VERSION 1.0.11 ------------------------- o Adding twitter account to README <2013-07-12 Fri> CHANGES IN VERSION 1.0.10 ------------------------- o clarify reamde <2013-07-08 Mon> o added Bioc2013 poster as static vignette <2013-07-12 Fri> CHANGES IN VERSION 1.0.9 ------------------------ o devel use clarification in readme <2013-07-08 Mon> o cite arXiv in vigette <2013-07-08 Mon> o cite R4P mailing list in vignette <2013-07-08 Mon> CHANGES IN VERSION 1.0.8 ------------------------ o rbioc-sig-proteomics group references in readme <2013-07-03 Wed> o added a twitter hook to the github repo <2013-07-03 Wed> o Sebastian is now contributor <2013-07-05 Fri> o Sebastian added new cleaver section in vignette <2013-07-05 Fri> o document useDevel in README.md <2013-07-05 Fri> CHANGES IN VERSION 1.0.7 ------------------------ o updated README.md and added TM repo to vignette <2013-07-02 Tue> CHANGES IN VERSION 1.0.6 ------------------------ o Updated bib file and added CITATION <2013-06-07 Fri> CHANGES IN VERSION 1.0.5 ------------------------ o MALDIquant: remove misleading length calls by Sebastian Gibb <2013-05-24 Fri> CHANGES IN VERSION 1.0.4 ------------------------ o importBrukerFlex: set verbose=FALSE, contributed by Sebastian Gibb <2013-05-01 Wed> CHANGES IN VERSION 1.0.3 ------------------------ o Updates in the MALDIquant section, contributed by Sebastian Gibb <2013-04-26 Fri> CHANGES IN VERSION 1.0.2 ------------------------ o update in vignette NetCDF installation <2013-04-19 Fri> o more similar updates <2013-04-24 Wed> CHANGES IN VERSION 1.0.1 ------------------------ o fixed 'doc/vigsrc/' to 'doc/vigsrc' in vignette <2013-04-09 Tue> o typos and installation section in vignette <2013-04-09 Tue> CHANGES IN VERSION 1.0.0 ------------------------ o bumping version for stable release <2013-04-06 Sat> o Adding rTANDEM as Suggests <2013-04-06 Sat> o Update and rebuild vignette with R 3.0.0 stable <2013-04-06 Sat> CHANGES IN VERSION 0.99.3 ------------------------- o Bioc version bump CHANGES IN VERSION 0.99.2 ------------------------- o removing rTANDEM from Suggests, as the package currently fails to build and results in R4P checking errors. Will add it again when builds <2013-02-20 Wed> CHANGES IN VERSION 0.99.1 ------------------------- o adding pre-build vignette <2013-02-20 Wed> CHANGES IN VERSION 0.99.0 ------------------------- o typo in startup msg <2013-01-09 Wed> o update README.md with R-2.15.2 installation instructions <2013-01-09 Wed> o Major updates to vignette <2013-02-15 Fri> o Added rTANDEM <2013-02-15 Fri> CHANGES IN VERSION 0.2.2 ------------------------ o removed Makefile from .Rbuildignore <2012-10-22 Mon> o Using mzXML from ProteomeXchange repo <2012-10-23 Tue> o using parallel quant <2012-10-23 Tue> CHANGES IN VERSION 0.2.1 ------------------------ o added visible library("MSnbase") in vignette <2012-10-17 Wed> CHANGES IN VERSION 0.2.0 ------------------------ o Added NEWS file <2012-10-05 Fri>