- Clearn up .gitignore and .Rbuildignore (in the hope to fix the 'figure not found error')
- Change paths to figures.
- New Bioc devel version.
- Using
knitr::include_graphics()to include figures.
- I give up: remove that effing figure that is supposedly not found despite being there.
- Fix syntax to fix missing figure error.
- Adapt vignette for new hpar version.
- New Bioc devel verison.
- Remove failing code chunk.
- Repeat ensembl mart connection until successful.
- Add links to R4MS.
- Remove XTandom, MSGF and isobar sections.
- Remove MSMap
- Fix mztab file name (required for new rpx)
- New version for Bioc 3.14 (devel)
- New version for Bioc 3.13 (release)
- 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.
- Specify
MSnID::peptides()(see also vladpetyuk/MSnID#12).
- Remove deprecated IPPD dependency
- Fix build errors
- remove getThermoHelaPRTC function (server down) <2019-10-24 Thu>
- Fix roxygen/namespace mess
- Use BiocManager
- Fix typo in rmd
- New Bioconductor devel version
- New Bioconductor release version
- Fix/update vignettes <2018-01-12 Fri>
- Add mention of DEP package <2018-01-13 Sat>
- New Bioc devel version
- New Bioc release version
- Bump to sync with Bioc <2017-10-19 Thu>
- 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>
- New devel version
- Fix failing vignette <2017-04-18 Tue>
- Update static vignette <2017-04-18 Tue>
- New devel version
- Suggest genefilter <2016-10-15 Sat>
- Update/compile static vignette for new release <2016-10-07 Fri>
- Fix typo <2016-03-01 Tue>
- updated msDataTab
- 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>
- 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>
- Fix vignette for mzTab v0.9 <2015-09-30 Wed>
- Added ReproducibleResearch biocView <2015-06-08 Mon>
- Update to MALDIquant 1.12 <2015-06-12 Fri>
- Bioc 3.2 devel
- Bioc 3.1 release
- recompile r4p vignette and add ref to vis vignette [2015-03-23 Mon]
- make RProtVis static due to hangs [2015-03-24 Tue]
- Vignette updates: simple R plots [2015-02-21 Sat]
- suggest rmarkdown (used to render vis vignette) [2015-02-12 Thu]
- don't require GNU make [2015-02-11 Wed]
- more vis vig updates [2015-01-28 Wed]
- added MS animations [2015-01-29 Thu]
- document workflows [2015-01-30 Fri]
- 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]
- Bioc release version bump
- cache package info [2014-11-15 Sat]
- update vignette and fixing errors [2014-10-31 Fri]
- new devel version for Bioc 3.1
- new release version for Bioc 3.0
- remove github link to MSGFgui since it has now been accepted [2014-10-03 Fri]
- new MSnID section [2014-10-04 Sat]
- mzR ident section [2014-10-01 Wed]
- HUPO2014 poster [2014-10-02 Thu]
- new MSGF+/gui sections contributed by Thomas [2014-10-01 Wed]
- 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]
- Using BiocStyle [2014-08-16 Sat]
- Many more sections to RProtVis vignette [2014-08-13 Wed]
- 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]
- 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]
- pxr renamed rpx [2014-03-28]
- using pxr to download data from the PX repository [2014-03-24 Mon]
- new downloadData and getThermoHelaPRTC functions [2013-12-14 Sat]
- 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>
- Moving cleaver to enhances to all building on Bioc release <2013-07-19 Fri>
- Adding twitter account to README <2013-07-12 Fri>
- clarify reamde <2013-07-08 Mon>
- added Bioc2013 poster as static vignette <2013-07-12 Fri>
- 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>
- 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>
- updated README.md and added TM repo to vignette <2013-07-02 Tue>
- Updated bib file and added CITATION <2013-06-07 Fri>
- MALDIquant: remove misleading length calls by Sebastian Gibb <2013-05-24 Fri>
- importBrukerFlex: set verbose=FALSE, contributed by Sebastian Gibb <2013-05-01 Wed>
- Updates in the MALDIquant section, contributed by Sebastian Gibb <2013-04-26 Fri>
- update in vignette NetCDF installation <2013-04-19 Fri>
- more similar updates <2013-04-24 Wed>
- fixed 'doc/vigsrc/' to 'doc/vigsrc' in vignette <2013-04-09 Tue>
- typos and installation section in vignette <2013-04-09 Tue>
- 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>
- Bioc version bump
- 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>
- adding pre-build vignette <2013-02-20 Wed>
- 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>
- removed Makefile from .Rbuildignore <2012-10-22 Mon>
- Using mzXML from ProteomeXchange repo <2012-10-23 Tue>
- using parallel quant <2012-10-23 Tue>
- added visible library("MSnbase") in vignette <2012-10-17 Wed>
- Added NEWS file <2012-10-05 Fri>