NEWS.md
In lgatto/RforProteomics: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication

RforProteomics 1

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 https://github.com/vladpetyuk/MSnID/issues/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>

RforProteomics 0.99

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>

lgatto/RforProteomics documentation built on May 10, 2023, 11:51 p.m.

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