NEWS

---

pRolocdata 1.49.1

• New version for devel

pRolocdata 1.49.0

• New version for devel

pRolocdata 1.45.1

• Lisa Breckels is now maintainer.

pRolocdata 1.45.0

• new devel version

pRolocdata 1.43.3

• Add [exprsFile|fdataFile|pdataFile].csv Dunkley2006.csv.gz and hyperLOPIT-SIData-ms3-rep12-intersect.csv.gz back to inst/extdata (needed to MSnbase vignette and tests).

pRolocdata 1.43.2

• add two files back to inst/extdata, needed for the pRoloc v01 and v02 vignettes.

pRolocdata 1.43.1

• move content of inst/extdata to the pRolocdata dataverse (https://dataverse.uclouvain.be/dataverse/pRolocdata).

pRolocdata 1.43.0

• new devel version

pRolocdata 1.42.0

• new release version

pRolocdata 1.37.1

• add data from Moloney et al. (2023)
• update syntax in the author field of description
• remove redundant alias for itzhak2016

pRolocdata 1.37.0

• new devel version for Bioc

pRolocdata 1.33.1

• Add hyperLOPIT2015_se data
• Add mulvey2015_se and mulvey2015norm_se data
• Regenerated README to include new datasets

pRolocdata 1.29.1

• merge github master

pRolocdata 1.27.3

• add THP-1 data from Mulvey and Breckels (2021)

pRolocdata 1.27.2

• add data from Courtland et al. (2020)

pRolocdata 1.27.1

• add data from Kozik et al. (2020)

pRolocdata 1.25.3

• update email

pRolocdata 1.25.2

• add data from Shin et al. (2020)
• add data from Baryluk et al. (2020)

pRolocdata 1.25.1

• add dynamic Itzhak data

pRolocdata 1.21.1

• Clarify that itzhak2017 data is LFQ from suppl table 3 <2018-11-06 Tue>
• Data from Krahmer et al. 2018 <2018-12-22 Sat>
• Data from Davies at al. 2018 <2019-02-01 Fri>

pRolocdata 1.21.0

• New version for Bioc 3.9 (devel)

pRolocdata 1.20.0

• New version for Bioc 3.8 (release)

pRolocdata 1.19.5

• Fix typos

pRolocdata 1.19.4

• New yeast spatial proteome dataset <2018-08-14 Tue>

pRolocdata 1.19.3

• New synechocystis spatial proteome <2018-07-26 Thu>

pRolocdata 1.19.2

• Fix typo in beltran2016 man page <2018-07-24 Tue>
• Added LOPIT-DC and hyperLOPIT U2OS data <2018-07-25 Wed>

pRolocdata 1.19.1

• Adding hyperLOPIT TAGM results <2018-05-21 Mon>

pRolocdata 1.19.0

• New Bioconductor devel version

pRolocdata 1.18.0

• New Bioconductor release version

pRolocdata 1.17.4

• Typo in tlopt colnames fixed for f1000 workflow <2018-04-10 Tue>

pRolocdata 1.17.3

• Add Proteome biocView <2018-04-05 Thu>

pRolocdata 1.17.2

• Add data from Beltran et al. 2016 <2018-03-17 Sat>
• Add data from Hirst et al. 2018 <2018-03-18 Sun>
• Add data from Itzhal et al. 2017 <2018-03-20 Tue>

pRolocdata 1.17.1

• Update README with information on how to add data <2018-03-08 Thu>

pRolocdata 1.13.2

• new U2OS hyperLOPIT data <2017-02-16 Thu>

pRolocdata 1.13.1

• Added the hyperLOPIT PMS-level data for MS3 replicates 1 and 2 and MS2 acquisitions, names 'hyperLOPIT2015ms3r1psm', 'hyperLOPIT2015ms3r2psm' and 'hyperLOPIT2015ms2psm' respectively. <2017-01-17 Tue>
• Added LOPIMS data for synapter 2.0 release: lopmisSyn1, lopimsSyn2 and lopimsSyn2_0frags <2017-01-18 Wed>

pRolocdata 1.13.0

• Bioc 3.5 devel

pRolocdata 1.12.0

• Bioc 3.4 release

pRolocdata 1.11.9

• rename andy2011 HEK293T2011 <2016-09-23 Fri>

pRolocdata 1.11.8

• rename andreyev2009 to andreyev2010 <2016-09-12 Mon>

pRolocdata 1.11.7

• Update title from Rodriguez-Pineiro et al. 2012 <2016-09-06 Tue>
• added data from bioc pRoloc workflow <2016-09-08 Thur>

pRolocdata 1.11.6

• Add combined trotter2010 data and markers fcol <2016-09-02 Fri>
• Add data from Rodriguez-Pineiro et al. 2012 <2016-09-02 Fri>

pRolocdata 1.11.5

• Added data from Andreyev et al. 2009 <2016-08-31 Wed>

pRolocdata 1.11.4

• Normalise manual titles <2016-08-16 Tue>
• Updated hyperLOPIT markers and goCC dataset <2016-08-22 Mon>

pRolocdata 1.11.3

• Added data from Stekhoven et al. 2014 <2016-08-12 Fri>

pRolocdata 1.11.2

• mv itzhak2016stcSILAC in right location <2016-08-10 Wed>

pRolocdata 1.11.1

• Added TL parameters for E15TG2a from Breckels et al. 2016 [2016-06-29 Wed]
• Added hyperLOPIT2015goCC binary GO CC [2016-06-29 Wed]
• Added data from Itzhak et al. 2016 <2016-08-10 Wed>

pRolocdata 1.9.5

• Added data from Mulvey et al. 2015 <2016-04-04 Mon>

pRolocdata 1.9.4

• Added the STRING-db tab delimitated PPI data for transfer learning example <2016-02-29 Mon>

pRolocdata 1.9.3

• data unit tests <2016-02-09 Tue>

pRolocdata 1.9.2

• fixed bug in E14TG2aS1 fData [2015-08-02 Mon]

pRolocdata 1.9.1

• added fraction information to hyperLOPIT data [2015-11-04 Wed]
• reverted fraction order, fixed bug in hyperLOPIT make script [2015-11-05 Thu]
• Added fraction number order [2015-11-05 Thu]

pRolocdata 1.9.0

• New version for Bio devel 3.3

pRolocdata 1.8.0

• New version for Bio release 3.2

pRolocdata 1.7.4

• new hyperLOPIT datasets on mouse stem cells [2015-10-07 Wed]

pRolocdata 1.7.3

• Fix typo in man pages [2015-09-08 Tue]

pRolocdata 1.7.2

• added HPA, GOCC and YLOC datasets from Breckels et al 2015 and all optimised parameters [2015-07-16 Thu]

pRolocdata 1.7.1

• update tan2009 data [2015-04-17 Fri]
• update dunkley2006, fixing named fData()$fcol fvars [2015-04-18 Sat]

pRolocdata 1.7.0

• new devel version for Bioc 3.2

pRolocdata 1.5.8

• added transfer learning results from Breckels et al 2015 to experimentData [2015-04-07 Thu]

pRolocdata 1.5.7

• added results from transfer learning from Breckels et al 2015 to E14TG2a datasets [2015-03-23 Mon]
• added knntl and svmtl parameters used for classification to experimentData slot in E14TG2aS1 dataset [2015-03-26 Thu]

pRolocdata 1.5.6

• using UniProt accession numbers as feature names for andy2011 and andy2011goCC [2015-03-21 Sat]

pRolocdata 1.5.5

• added GO CC auxiliary data [2015-02-05 Thu]
• added pData(havugimana2012) [2015-02-10 Tue]

pRolocdata 1.5.4

• protein complex gradient data: fabre2015 (2 reps), havugimana2012, kirkwood2013 and kristensen2012 (3 reps) [2015-02-04 Wed]

pRolocdata 1.5.3

• Updating Groen 2014 man title [2014-12-12 Fri]
• Update biocViews [2014-12-12 Fri]

pRolocdata 1.5.2

• Nothing

pRolocdata 1.5.1

• Updated all markers in andy, dunkley and tan datasets and old marker column in fData renamed markers.orig [2014-10-30 Thu]
• New E14TG2a datasets added [2014-10-30 Thu]
• Doc on boosting markers [2014-10-30 Thu]
• Fixed exprs data in E14 datasets [2014-11-07 Fri]

pRolocdata 1.5.0

• new devel version

pRolocdata 1.3.5

• Remove new/meta pRolocmetadata <2014-09-03 Wed>
• Updated fData in Groen datasets <2014-09-23 Tue>

pRolocdata 1.3.4

• Replaced Human by Homo sapiens [2014-09-02 Tue]

pRolocdata 1.3.3

• Updated README.md (generated from README.Rmd) [2014-08-29 Fri]
• pRolocmetadata infrastructure [2014-08-29 Fri]
• updated all datasets with appropriate pRolocmetadata [2014-08-29 Fri]

pRolocdata 1.3.2

• added experimentData(nikolovski2014) [2014-08-28 Thu]

pRolocdata 1.3.1

• Data from Nikolovski et al. 2014 (PMID 25122472) [2014-08-28 Thu] p gzipped all csv files in inst/extdata [2014-08-28 Thu]

pRolocdata 1.0.7

• added Uniprot accesion number and entry names to Tan datasets <2013-03-10 Mon>
• move pRoloc/inst/extdata/*csv here [2014-03-23 Sun]
• import MSnbase in NAMESPACE [2014-03-23 Sun]

pRolocdata 1.0.6

• new data from Groen et al <2013-12-20 Fri>

pRolocdata 1.0.5

• changed featureNames(tan2006r*) to FBgn numbers <2013-12-16 Mon>

pRolocdata 1.0.4

• Bioc 2.14 version bump

pRolocdata 1.0.3

• Bioc 2.13 version bump

pRolocdata 1.0.2

• new data from Hall et al 2009 <2013-10-01 Tue>

pRolocdata 1.0.1

• changed featureNames(dunkley2006) to upper case <2013-09-17 Tue>

pRolocdata 1.0.0

• bumping version for stable release <2013-04-07 Sun>

pRolocdata 0.99.11

• Bioc 2.12 version bump

pRolocdata 0.99.10

• Fixed non ASCII warning <2013-03-19 Tue>

pRolocdata 0.99.9

• added column 'pd.validated' to datasets used in Breckels et al. with the organelle/protein family assignments manually assigned to each phenotype from UniprotKB. <2013-03-05 Tue>
• added data from Nikolovski et al 2012. <2013-03-13 Wed>
• removed column pd.validated and added new column to fData called pd.markers which contains all original organelle markers plus new protein markers found using phenoDisco as described in Breckels et al paper. <2013-03-18 Mon>
• updated fvarMetaData slot for all datasets used in Breckels et al paper <2013-03-18 Mon>
• updated nikolovski pData <2013-03-18 Mon>

pRolocdata 0.99.8

• added shallow (from Dunkley 2006) and steep (from Sadowski 2008) data set used in Trotter et al 2010. <2013-03-04 Mon>

pRolocdata 0.99.7

• New Andy2011 dataset on HEK293T added <2013-02-26 Tue>
• Updated all existing LOPIT datasets used in Breckels et al. (dunkley2006, tan2009r1) to include a column in the featureData of the phenoDisco output. <2013-02-26 Tue>
• Updated documentation for LOPIT datasets <2013-02-26 Tue>
• L Breckels added as author <2013-02-26 Tue>

pRolocdata 0.99.6

• Typo in tan man <2013-02-20 Wed>

pRolocdata 0.99.5

• renamed script names to be consistent with data names <2012-11-14 Wed>

pRolocdata 0.99.4

• Added pRoloc to Suggests <2012-09-16 Sun>

pRolocdata 0.99.3

• fixed at_chloro fvarMetadata reference and updated at_chloro example to produce at_chloro2 with percentages as in Ferro et al. 2010 <2012-09-15 Sat>

pRolocdata 0.99.2

• updated pRolocdata to use data (does not return a dataframe anymore) and startup message <2012-09-08 Sat>
• updated at_chloro exmaple <2012-09-08 Sat>

pRolocdata 0.99.1

• New at_chloro data set <2012-09-07 Fri>

pRolocdata 0.99.0

• Initial commit with data from Dunkley et al. (2006), Foster et al. (2006) and Tan et al. (2009). <2012-09-05 Wed>
• Removing pRoloc from Depends <2012-09-06 Thu>