Changes in version 1.39.2 - Clearn up .gitignore and .Rbuildignore (in the hope to fix the 'figure not found error') Changes in version 1.39.1 - Change paths to figures. Changes in version 1.39.0 - New Bioc devel version. Changes in version 1.37.4 - Using knitr::include_graphics() to include figures. Changes in version 1.37.3 - I give up: remove that effing figure that is supposedly not found despite being there. Changes in version 1.37.2 - Fix syntax to fix missing figure error. Changes in version 1.37.1 - Adapt vignette for new hpar version. Changes in version 1.37.0 - New Bioc devel verison. Changes in version 1.35.1 - Remove failing code chunk. Changes in version 1.33.1 - Repeat ensembl mart connection until successful. - Add links to R4MS. - Remove XTandom, MSGF and isobar sections. - Remove MSMap Changes in version 1.31.1 - Fix mztab file name (required for new rpx) Changes in version 1.31.0 - New version for Bioc 3.14 (devel) Changes in version 1.30.0 - New version for Bioc 3.13 (release) Changes in version 1.29.2 - Suggest rpx version 1.99.2 or later (to make use of caching and avoid repeated downloads). - Remove the shinyMA function. - Delete the code from the rTANDEM section, and only mention the package. - Remove synapter(data) suggestion. Changes in version 1.29.1 - Specify MSnID::peptides() (see also https://github.com/vladpetyuk/MSnID/issues/12). Changes in version 1.27.1 - Remove deprecated IPPD dependency Changes in version 1.25.1 - Fix build errors Changes in version 1.23.1 - remove getThermoHelaPRTC function (server down) <2019-10-24 Thu> Changes in version 1.19.4 - Fix roxygen/namespace mess Changes in version 1.19.3 - Use BiocManager - Fix typo in rmd Changes in version 1.19.0 - New Bioconductor devel version Changes in version 1.18.0 - New Bioconductor release version Changes in version 1.17.1 - Fix/update vignettes <2018-01-12 Fri> - Add mention of DEP package <2018-01-13 Sat> Changes in version 1.17.0 - New Bioc devel version Changes in version 1.16.0 - New Bioc release version Changes in version 1.15.2 - Bump to sync with Bioc <2017-10-19 Thu> Changes in version 1.15.1 - mstut functions <2017-06-27 Tue> - Move vignettes to Rmd/html <2017-06-27 Tue> - New vignette about proteomics package downloads <2017-06-29 Thu> Changes in version 1.15.0 - New devel version Changes in version 1.13.1 - Fix failing vignette <2017-04-18 Tue> - Update static vignette <2017-04-18 Tue> Changes in version 1.13.0 - New devel version Changes in version 1.11.4 - Suggest genefilter <2016-10-15 Sat> Changes in version 1.11.3 - Update/compile static vignette for new release <2016-10-07 Fri> - Fix typo <2016-03-01 Tue> Changes in version 1.9.3 - updated msDataTab Changes in version 1.9.2 - more edits to vignette <2015-12-01 Tue> - added Vlas's comprehensive real-life example to the vignette <2015-12-05 Sat> - update msDataTab <2015-12-05 Sat> Changes in version 1.9.1 - updated RforProteomics vignette <2015-11-30 Mon> - (unexported) msDataTable function to create a MS/prot data/objects table <2015-11-30 Mon> - add a short section for readMSnSet[2] <2015-12-01 Tue> Changes in version 1.7.2 - Fix vignette for mzTab v0.9 <2015-09-30 Wed> Changes in version 1.7.1 - Added ReproducibleResearch biocView <2015-06-08 Mon> - Update to MALDIquant 1.12 <2015-06-12 Fri> Changes in version 1.7.0 - Bioc 3.2 devel Changes in version 1.6.0 - Bioc 3.1 release Changes in version 1.5.9 - recompile r4p vignette and add ref to vis vignette [2015-03-23 Mon] - make RProtVis static due to hangs [2015-03-24 Tue] Changes in version 1.5.8 - Vignette updates: simple R plots [2015-02-21 Sat] Changes in version 1.5.7 - suggest rmarkdown (used to render vis vignette) [2015-02-12 Thu] Changes in version 1.5.6 - don't require GNU make [2015-02-11 Wed] Changes in version 1.5.5 - more vis vig updates [2015-01-28 Wed] - added MS animations [2015-01-29 Thu] - document workflows [2015-01-30 Fri] Changes in version 1.5.4 - rename ProtViz() to RProtVis/RProtViz to avoid confusion with the vignette name [2015-01-28 Wed] - RProtVis vignette updates [2015-01-27 Tue] - Use markdown::render [2015-01-27 Tue] Changes in version 1.5.3 - Bioc release version bump Changes in version 1.5.2 - cache package info [2014-11-15 Sat] Changes in version 1.5.1 - update vignette and fixing errors [2014-10-31 Fri] Changes in version 1.5.0 - new devel version for Bioc 3.1 Changes in version 1.4.0 - new release version for Bioc 3.0 Changes in version 1.3.8 - remove github link to MSGFgui since it has now been accepted [2014-10-03 Fri] - new MSnID section [2014-10-04 Sat] Changes in version 1.3.7 - mzR ident section [2014-10-01 Wed] - HUPO2014 poster [2014-10-02 Thu] Changes in version 1.3.6 - new MSGF+/gui sections contributed by Thomas [2014-10-01 Wed] Changes in version 1.3.5 - Proteomics workflow (from Bioc2014 workshop) [2014-08-17 Sun] - Mention viz vig requires Bioc >= 3.0 and link to on-line version [2014-08-27 Wed] - Link to shiyapps/shinyMA [2014-09-03 Wed] - added QC section [2014-10-01 Wed] Changes in version 1.3.4 - Using BiocStyle [2014-08-16 Sat] Changes in version 1.3.3 - Many more sections to RProtVis vignette [2014-08-13 Wed] Changes in version 1.3.2 - RforProteomics wiki on github [2014-08-02 Sat] - Proteomics viz vignette [2014-08-06 Wed] - shinyMA function [2014-08-07 Thu] - fix PXD000001 PRIDE urls [2014-08-08 Fri] - add protViz CRAN package to vig [2014-08-09 Sat] - RProtVis vignette needs MALDIquant >= 1.11 now [2014-08-11 Mon] Changes in version 1.3.1 - get biocView packages as a function [2014-07-23 Wed] - various typos and updates in vignette [2014-07-23 Wed] - functions to get packages for a biocView [2014-07-23 Wed] - relying on cache to reduce build time [2014-07-24 Thu] Changes in version 1.0.18 - pxr renamed rpx [2014-03-28] Changes in version 1.0.17 - using pxr to download data from the PX repository [2014-03-24 Mon] Changes in version 1.0.16 - new downloadData and getThermoHelaPRTC functions [2013-12-14 Sat] Changes in version 1.0.13 - Updates in the MALDIquant section <2013-09-08 Sun> - Fixed new warnings in vignette: cols - columns <2013-09-18 Wed> - do not cache package listing code <2013-09-19 Thu> Changes in version 1.0.12 - Moving cleaver to enhances to all building on Bioc release <2013-07-19 Fri> Changes in version 1.0.11 - Adding twitter account to README <2013-07-12 Fri> Changes in version 1.0.10 - clarify reamde <2013-07-08 Mon> - added Bioc2013 poster as static vignette <2013-07-12 Fri> Changes in version 1.0.9 - devel use clarification in readme <2013-07-08 Mon> - cite arXiv in vigette <2013-07-08 Mon> - cite R4P mailing list in vignette <2013-07-08 Mon> Changes in version 1.0.8 - rbioc-sig-proteomics group references in readme <2013-07-03 Wed> - added a twitter hook to the github repo <2013-07-03 Wed> - Sebastian is now contributor <2013-07-05 Fri> - Sebastian added new cleaver section in vignette <2013-07-05 Fri> - document useDevel in README.md <2013-07-05 Fri> Changes in version 1.0.7 - updated README.md and added TM repo to vignette <2013-07-02 Tue> Changes in version 1.0.6 - Updated bib file and added CITATION <2013-06-07 Fri> Changes in version 1.0.5 - MALDIquant: remove misleading length calls by Sebastian Gibb <2013-05-24 Fri> Changes in version 1.0.4 - importBrukerFlex: set verbose=FALSE, contributed by Sebastian Gibb <2013-05-01 Wed> Changes in version 1.0.3 - Updates in the MALDIquant section, contributed by Sebastian Gibb <2013-04-26 Fri> Changes in version 1.0.2 - update in vignette NetCDF installation <2013-04-19 Fri> - more similar updates <2013-04-24 Wed> Changes in version 1.0.1 - fixed 'doc/vigsrc/' to 'doc/vigsrc' in vignette <2013-04-09 Tue> - typos and installation section in vignette <2013-04-09 Tue> Changes in version 1.0.0 - bumping version for stable release <2013-04-06 Sat> - Adding rTANDEM as Suggests <2013-04-06 Sat> - Update and rebuild vignette with R 3.0.0 stable <2013-04-06 Sat> RforProteomics 0.99 Changes in version 0.99.3 - Bioc version bump Changes in version 0.99.2 - 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 - adding pre-build vignette <2013-02-20 Wed> Changes in version 0.99.0 - typo in startup msg <2013-01-09 Wed> - update README.md with R-2.15.2 installation instructions <2013-01-09 Wed> - Major updates to vignette <2013-02-15 Fri> - Added rTANDEM <2013-02-15 Fri> Changes in version 0.2.2 - removed Makefile from .Rbuildignore <2012-10-22 Mon> - Using mzXML from ProteomeXchange repo <2012-10-23 Tue> - using parallel quant <2012-10-23 Tue> Changes in version 0.2.1 - added visible library("MSnbase") in vignette <2012-10-17 Wed> Changes in version 0.2.0 - Added NEWS file <2012-10-05 Fri>