CHANGES IN VERSION 1.43.3 ------------------------- o 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). CHANGES IN VERSION 1.43.2 ------------------------- o add two files back to inst/extdata, needed for the pRoloc v01 and v02 vignettes. CHANGES IN VERSION 1.43.1 ------------------------- o move content of inst/extdata to the pRolocdata dataverse (https://dataverse.uclouvain.be/dataverse/pRolocdata). CHANGES IN VERSION 1.43.0 ------------------------- o new devel version CHANGES IN VERSION 1.42.0 ------------------------- o new release version CHANGES IN VERSION 1.37.1 ------------------------- o add data from Moloney et al. (2023) o update syntax in the author field of description o remove redundant alias for itzhak2016 CHANGES IN VERSION 1.37.0 ------------------------- o new devel version for Bioc CHANGES IN VERSION 1.33.1 ------------------------- o Add hyperLOPIT2015_se data o Add mulvey2015_se and mulvey2015norm_se data o Regenerated README to include new datasets CHANGES IN VERSION 1.29.1 ------------------------- o merge github master CHANGES IN VERSION 1.27.3 ------------------------- o add THP-1 data from Mulvey and Breckels (2021) CHANGES IN VERSION 1.27.2 ------------------------- o add data from Courtland et al. (2020) CHANGES IN VERSION 1.27.1 ------------------------- o add data from Kozik et al. (2020) CHANGES IN VERSION 1.25.3 ------------------------- o update email CHANGES IN VERSION 1.25.2 ------------------------- o add data from Shin et al. (2020) o add data from Baryluk et al. (2020) CHANGES IN VERSION 1.25.1 ------------------------- o add dynamic Itzhak data CHANGES IN VERSION 1.21.1 ------------------------- o Clarify that itzhak2017 data is LFQ from suppl table 3 <2018-11-06 Tue> o Data from Krahmer et al. 2018 <2018-12-22 Sat> o Data from Davies at al. 2018 <2019-02-01 Fri> CHANGES IN VERSION 1.21.0 ------------------------- o New version for Bioc 3.9 (devel) CHANGES IN VERSION 1.20.0 ------------------------- o New version for Bioc 3.8 (release) CHANGES IN VERSION 1.19.5 ------------------------- o Fix typos CHANGES IN VERSION 1.19.4 ------------------------- o New yeast spatial proteome dataset <2018-08-14 Tue> CHANGES IN VERSION 1.19.3 ------------------------- o New synechocystis spatial proteome <2018-07-26 Thu> CHANGES IN VERSION 1.19.2 ------------------------- o Fix typo in beltran2016 man page <2018-07-24 Tue> o Added LOPIT-DC and hyperLOPIT U2OS data <2018-07-25 Wed> CHANGES IN VERSION 1.19.1 ------------------------- o Adding hyperLOPIT TAGM results <2018-05-21 Mon> CHANGES IN VERSION 1.19.0 ------------------------- o New Bioconductor devel version CHANGES IN VERSION 1.18.0 ------------------------- o New Bioconductor release version CHANGES IN VERSION 1.17.4 ------------------------- o Typo in tlopt colnames fixed for f1000 workflow <2018-04-10 Tue> CHANGES IN VERSION 1.17.3 ------------------------- o Add Proteome biocView <2018-04-05 Thu> CHANGES IN VERSION 1.17.2 ------------------------- o Add data from Beltran et al. 2016 <2018-03-17 Sat> o Add data from Hirst et al. 2018 <2018-03-18 Sun> o Add data from Itzhal et al. 2017 <2018-03-20 Tue> CHANGES IN VERSION 1.17.1 ------------------------- o Update README with information on how to add data <2018-03-08 Thu> CHANGES IN VERSION 1.13.2 ------------------------- o new U2OS hyperLOPIT data <2017-02-16 Thu> CHANGES IN VERSION 1.13.1 ------------------------- o 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> o Added LOPIMS data for synapter 2.0 release: lopmisSyn1, lopimsSyn2 and lopimsSyn2_0frags <2017-01-18 Wed> CHANGES IN VERSION 1.13.0 ------------------------- o Bioc 3.5 devel CHANGES IN VERSION 1.12.0 ------------------------- o Bioc 3.4 release CHANGES IN VERSION 1.11.9 ------------------------- o rename andy2011 HEK293T2011 <2016-09-23 Fri> CHANGES IN VERSION 1.11.8 ------------------------- o rename andreyev2009 to andreyev2010 <2016-09-12 Mon> CHANGES IN VERSION 1.11.7 ------------------------- o Update title from Rodriguez-Pineiro et al. 2012 <2016-09-06 Tue> o added data from bioc pRoloc workflow <2016-09-08 Thur> CHANGES IN VERSION 1.11.6 ------------------------- o Add combined trotter2010 data and markers fcol <2016-09-02 Fri> o Add data from Rodriguez-Pineiro et al. 2012 <2016-09-02 Fri> CHANGES IN VERSION 1.11.5 ------------------------- o Added data from Andreyev et al. 2009 <2016-08-31 Wed> CHANGES IN VERSION 1.11.4 ------------------------- o Normalise manual titles <2016-08-16 Tue> o Updated hyperLOPIT markers and goCC dataset <2016-08-22 Mon> CHANGES IN VERSION 1.11.3 ------------------------- o Added data from Stekhoven et al. 2014 <2016-08-12 Fri> CHANGES IN VERSION 1.11.2 ------------------------- o mv itzhak2016stcSILAC in right location <2016-08-10 Wed> CHANGES IN VERSION 1.11.1 ------------------------- o Added TL parameters for E15TG2a from Breckels et al. 2016 [2016-06-29 Wed] o Added hyperLOPIT2015goCC binary GO CC [2016-06-29 Wed] o Added data from Itzhak et al. 2016 <2016-08-10 Wed> CHANGES IN VERSION 1.9.5 ------------------------ o Added data from Mulvey et al. 2015 <2016-04-04 Mon> CHANGES IN VERSION 1.9.4 ------------------------ o Added the STRING-db tab delimitated PPI data for transfer learning example <2016-02-29 Mon> CHANGES IN VERSION 1.9.3 ------------------------ o data unit tests <2016-02-09 Tue> CHANGES IN VERSION 1.9.2 ------------------------ o fixed bug in E14TG2aS1 fData [2015-08-02 Mon] CHANGES IN VERSION 1.9.1 ------------------------ o added fraction information to hyperLOPIT data [2015-11-04 Wed] o reverted fraction order, fixed bug in hyperLOPIT make script [2015-11-05 Thu] o Added fraction number order [2015-11-05 Thu] CHANGES IN VERSION 1.9.0 ------------------------ o New version for Bio devel 3.3 CHANGES IN VERSION 1.8.0 ------------------------ o New version for Bio release 3.2 CHANGES IN VERSION 1.7.4 ------------------------ o new hyperLOPIT datasets on mouse stem cells [2015-10-07 Wed] CHANGES IN VERSION 1.7.3 ------------------------ o Fix typo in man pages [2015-09-08 Tue] CHANGES IN VERSION 1.7.2 ------------------------ o added HPA, GOCC and YLOC datasets from Breckels et al 2015 and all optimised parameters [2015-07-16 Thu] CHANGES IN VERSION 1.7.1 ------------------------ o update tan2009 data [2015-04-17 Fri] o update dunkley2006, fixing named fData()$fcol fvars [2015-04-18 Sat] CHANGES IN VERSION 1.7.0 ------------------------ o new devel version for Bioc 3.2 CHANGES IN VERSION 1.5.8 ------------------------ o added transfer learning results from Breckels et al 2015 to experimentData [2015-04-07 Thu] CHANGES IN VERSION 1.5.7 ------------------------ o added results from transfer learning from Breckels et al 2015 to E14TG2a datasets [2015-03-23 Mon] o added knntl and svmtl parameters used for classification to experimentData slot in E14TG2aS1 dataset [2015-03-26 Thu] CHANGES IN VERSION 1.5.6 ------------------------ o using UniProt accession numbers as feature names for andy2011 and andy2011goCC [2015-03-21 Sat] CHANGES IN VERSION 1.5.5 ------------------------ o added GO CC auxiliary data [2015-02-05 Thu] o added pData(havugimana2012) [2015-02-10 Tue] CHANGES IN VERSION 1.5.4 ------------------------ o protein complex gradient data: fabre2015 (2 reps), havugimana2012, kirkwood2013 and kristensen2012 (3 reps) [2015-02-04 Wed] CHANGES IN VERSION 1.5.3 ------------------------ o Updating Groen 2014 man title [2014-12-12 Fri] o Update biocViews [2014-12-12 Fri] CHANGES IN VERSION 1.5.2 ------------------------ o Nothing CHANGES IN VERSION 1.5.1 ------------------------ o Updated all markers in andy, dunkley and tan datasets and old marker column in fData renamed markers.orig [2014-10-30 Thu] o New E14TG2a datasets added [2014-10-30 Thu] o Doc on boosting markers [2014-10-30 Thu] o Fixed exprs data in E14 datasets [2014-11-07 Fri] CHANGES IN VERSION 1.5.0 ------------------------ o new devel version CHANGES IN VERSION 1.3.5 ------------------------ o Remove new/meta pRolocmetadata <2014-09-03 Wed> o Updated fData in Groen datasets <2014-09-23 Tue> CHANGES IN VERSION 1.3.4 ------------------------ o Replaced Human by Homo sapiens [2014-09-02 Tue] CHANGES IN VERSION 1.3.3 ------------------------ o Updated README.md (generated from README.Rmd) [2014-08-29 Fri] o pRolocmetadata infrastructure [2014-08-29 Fri] o updated all datasets with appropriate pRolocmetadata [2014-08-29 Fri] CHANGES IN VERSION 1.3.2 ------------------------ o added experimentData(nikolovski2014) [2014-08-28 Thu] CHANGES IN VERSION 1.3.1 ------------------------ o Data from Nikolovski et al. 2014 (PMID 25122472) [2014-08-28 Thu] p gzipped all csv files in inst/extdata [2014-08-28 Thu] CHANGES IN VERSION 1.0.7 ------------------------ o added Uniprot accesion number and entry names to Tan datasets <2013-03-10 Mon> o move pRoloc/inst/extdata/*csv here [2014-03-23 Sun] o import MSnbase in NAMESPACE [2014-03-23 Sun] CHANGES IN VERSION 1.0.6 ------------------------ o new data from Groen et al <2013-12-20 Fri> CHANGES IN VERSION 1.0.5 ------------------------ o changed featureNames(tan2006r*) to FBgn numbers <2013-12-16 Mon> CHANGES IN VERSION 1.0.4 ------------------------ o Bioc 2.14 version bump CHANGES IN VERSION 1.0.3 ------------------------ o Bioc 2.13 version bump CHANGES IN VERSION 1.0.2 ------------------------ o new data from Hall et al 2009 <2013-10-01 Tue> CHANGES IN VERSION 1.0.1 ------------------------ o changed featureNames(dunkley2006) to upper case <2013-09-17 Tue> CHANGES IN VERSION 1.0.0 ------------------------ o bumping version for stable release <2013-04-07 Sun> CHANGES IN VERSION 0.99.11 -------------------------- o Bioc 2.12 version bump CHANGES IN VERSION 0.99.10 -------------------------- o Fixed non ASCII warning <2013-03-19 Tue> CHANGES IN VERSION 0.99.9 ------------------------- o 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> o added data from Nikolovski et al 2012. <2013-03-13 Wed> o 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> o updated fvarMetaData slot for all datasets used in Breckels et al paper <2013-03-18 Mon> o updated nikolovski pData <2013-03-18 Mon> CHANGES IN VERSION 0.99.8 ------------------------- o added shallow (from Dunkley 2006) and steep (from Sadowski 2008) data set used in Trotter et al 2010. <2013-03-04 Mon> CHANGES IN VERSION 0.99.7 ------------------------- o New Andy2011 dataset on HEK293T added <2013-02-26 Tue> o 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> o Updated documentation for LOPIT datasets <2013-02-26 Tue> o L Breckels added as author <2013-02-26 Tue> CHANGES IN VERSION 0.99.6 ------------------------- o Typo in tan man <2013-02-20 Wed> CHANGES IN VERSION 0.99.5 ------------------------- o renamed script names to be consistent with data names <2012-11-14 Wed> CHANGES IN VERSION 0.99.4 ------------------------- o Added pRoloc to Suggests <2012-09-16 Sun> CHANGES IN VERSION 0.99.3 ------------------------- o 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> CHANGES IN VERSION 0.99.2 ------------------------- o updated pRolocdata to use data (does not return a dataframe anymore) and startup message <2012-09-08 Sat> o updated at_chloro exmaple <2012-09-08 Sat> CHANGES IN VERSION 0.99.1 ------------------------- o New at_chloro data set <2012-09-07 Fri> CHANGES IN VERSION 0.99.0 ------------------------- o Initial commit with data from Dunkley et al. (2006), Foster et al. (2006) and Tan et al. (2009). <2012-09-05 Wed> o Removing pRoloc from Depends <2012-09-06 Thu>