# RforProteomics 1

## Changes in version 1.51.1

- Remove defunct readMzTab reading. Replace by
  readSummarizedExperiment() and convert to MSnSet.
- Update startup message and point to RforMS.

## Changes in version 1.49.1

- Remove rols dep.

## Changes in version 1.47.2

- Use latest MSnbase

## Changes in version 1.47.1

- Remove DEP suggests.
- Update vignettes: remove some references to old/outdated packages,
  add note about RforMS.

## 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>
