RforProteomics 1.0

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

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>