Files in lgatto/pRolocdata
Data accompanying the pRoloc package
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/data.R
R/zzz.R
README.Rmd
README.md
data/Barylyuk2020ToxoLopit.rda
data/E14TG2aR.RData
data/E14TG2aS1.RData
data/E14TG2aS1goCC.rda
data/E14TG2aS1yLoc.rda
data/E14TG2aS2.RData
data/HEK293T2011.RData
data/HEK293T2011goCC.rda
data/HEK293T2011hpa.rda
data/Kozik_con.rda
data/Kozik_pra.rda
data/Kozik_tam.rda
data/Shin2019MitoControlrep1.rda
data/Shin2019MitoControlrep2.rda
data/Shin2019MitoControlrep3.rda
data/Shin2019MitoGcc88rep1.rda
data/Shin2019MitoGcc88rep2.rda
data/Shin2019MitoGcc88rep3.rda
data/Shin2019MitoGol97rep1.rda
data/Shin2019MitoGol97rep2.rda
data/Shin2019MitoGol97rep3.rda
data/andreyev2010.rda
data/andreyev2010activ.rda
data/andreyev2010rest.rda
data/andy2011.RData
data/andy2011goCC.rda
data/andy2011hpa.rda
data/at_chloro.rda
data/baers2018.rda
data/beltran2016HCMV120.rda
data/beltran2016HCMV24.rda
data/beltran2016HCMV48.rda
data/beltran2016HCMV72.rda
data/beltran2016HCMV96.rda
data/beltran2016MOCK120.rda
data/beltran2016MOCK24.rda
data/beltran2016MOCK48.rda
data/beltran2016MOCK72.rda
data/beltran2016MOCK96.rda
data/courtland_control.rda
data/courtland_mutant.rda
data/davies2018ap4b1.rda
data/davies2018ap4e1.rda
data/davies2018wt.rda
data/dunkley2006.RData
data/dunkley2006goCC.RData
data/fabre2015r1.rda
data/fabre2015r2.rda
data/foster2006.RData
data/groen2014cmb.RData
data/groen2014r1.RData
data/groen2014r1goCC.RData
data/groen2014r2.RData
data/groen2014r3.RData
data/hall2009.rda
data/havugimana2012.rda
data/hirst2018.rda
data/hyperLOPIT2015.RData
data/hyperLOPIT2015_se.rda
data/hyperLOPIT2015goCC.RData
data/hyperLOPIT2015ms2.RData
data/hyperLOPIT2015ms2psm.rda
data/hyperLOPIT2015ms3r1.RData
data/hyperLOPIT2015ms3r1psm.rda
data/hyperLOPIT2015ms3r2.RData
data/hyperLOPIT2015ms3r2psm.rda
data/hyperLOPIT2015ms3r3.RData
data/hyperLOPITU2OS2017.rda
data/hyperLOPITU2OS2017b.rda
data/hyperLOPITU2OS2018.RData
data/itzhak2016helaCtrl.rda
data/itzhak2016helaEgf.rda
data/itzhak2016stcSILAC.rda
data/itzhak2017.rda
data/itzhak2017markers.rda
data/kirkwood2013.rda
data/krahmer2018pcp.rda
data/krahmer2018phosphopcp.rda
data/kristensen2012r1.rda
data/kristensen2012r2.rda
data/kristensen2012r3.rda
data/lopimsSyn1.rda
data/lopimsSyn2.rda
data/lopimsSyn2_0frags.rda
data/lopitdcU2OS2018.RData
data/lpsTimecourse_mulvey2021.RData
data/lpsTimecourse_rep1_mulvey2021.RData
data/lpsTimecourse_rep2_mulvey2021.RData
data/lpsTimecourse_rep3_mulvey2021.RData
data/moloneyTbBSF.RData
data/moloneyTbPCF.RData
data/moloneyTcBSF.RData
data/moloneyTcPCF.RData
data/mulvey2015.rda
data/mulvey2015_se.rda
data/mulvey2015norm.rda
data/mulvey2015norm_se.rda
data/nikolovski2012.RData
data/nikolovski2012imp.RData
data/nikolovski2014.rda
data/orre2019a431.rda
data/orre2019h322.rda
data/orre2019hcc827.rda
data/orre2019hcc827gef.rda
data/orre2019hcc827rep1.rda
data/orre2019hcc827rep2.rda
data/orre2019hcc827rep3.rda
data/orre2019mcf7.rda
data/orre2019u251.rda
data/psms_lpsTimecourse_rep1_mulvey2021.RData
data/psms_lpsTimecourse_rep2_mulvey2021.RData
data/psms_lpsTimecourse_rep3_mulvey2021.RData
data/psms_thpLOPIT_lps_rep1_set1.RData
data/psms_thpLOPIT_lps_rep1_set2.RData
data/psms_thpLOPIT_lps_rep2_set1.RData
data/psms_thpLOPIT_lps_rep2_set2.RData
data/psms_thpLOPIT_lps_rep3_set1.RData
data/psms_thpLOPIT_lps_rep3_set2.RData
data/psms_thpLOPIT_unstim_rep1_set1.RData
data/psms_thpLOPIT_unstim_rep1_set2.RData
data/psms_thpLOPIT_unstim_rep2_set1.RData
data/psms_thpLOPIT_unstim_rep2_set2.RData
data/psms_thpLOPIT_unstim_rep3_set1.RData
data/psms_thpLOPIT_unstim_rep3_set2.RData
data/rodriguez2012r1.rda
data/rodriguez2012r2.rda
data/rodriguez2012r3.rda
data/stekhoven2014.rda
data/tan2009r1.RData
data/tan2009r1goCC.RData
data/tan2009r2.RData
data/tan2009r3.RData
data/thpLOPIT_lps_mulvey2021.RData
data/thpLOPIT_lps_rep1_mulvey2021.RData
data/thpLOPIT_lps_rep2_mulvey2021.RData
data/thpLOPIT_lps_rep3_mulvey2021.RData
data/thpLOPIT_unstimulated_mulvey2021.RData
data/thpLOPIT_unstimulated_rep1_mulvey2021.RData
data/thpLOPIT_unstimulated_rep2_mulvey2021.RData
data/thpLOPIT_unstimulated_rep3_mulvey2021.RData
data/trotter2010.rda
data/trotter2010shallow.rda
data/trotter2010steep.rda
data/yeast2018.RData
inst/extdata/1-s2.0-S2211124717311889-mmc3.xlsx
inst/extdata/1-s2.0-S2405471216302897-mmc4.xlsx
inst/extdata/20220304_TbBSF_n3_output.csv.gz
inst/extdata/20220304_TbPCF_n3_output.csv.gz
inst/extdata/20220304_TcBSF_n3_output.csv.gz
inst/extdata/20220304_TcPCF_n3_output.csv.gz
inst/extdata/22863883_Rep1.txt.gz
inst/extdata/22863883_Rep2.txt.gz
inst/extdata/22863883_Rep3.txt.gz
inst/extdata/22939629.txt.gz
inst/extdata/24043423.txt.gz
inst/extdata/245589ST2_protein_distributions.csv.gz
inst/extdata/245589ST3_MarkerList_250614.csv.gz
inst/extdata/245589ST4_SVMLocalisation_280514.csv.gz
inst/extdata/25561571_Rep1.txt.gz
inst/extdata/25561571_Rep2.txt.gz
inst/extdata/41467_2018_6172_MOESM3_ESM.xlsx
inst/extdata/A431.csv
inst/extdata/AT_CHLORO_table_120906.csv.gz
inst/extdata/Andreyev2009_Supplemental_Table_S1-L-C.csv.gz
inst/extdata/Andreyev2009_Supplemental_Table_S2-L-C-EAD.csv.gz
inst/extdata/Daviesetal.csv
inst/extdata/Dunkley2006.csv.gz
inst/extdata/E14TG2a_2011.tar.gz
inst/extdata/Groen_MarkerList.csv
inst/extdata/Groen_Supplemental_Table2.csv
inst/extdata/Groen_Supplemental_Table3a.csv.gz
inst/extdata/Groen_Supplemental_Table3b.csv.gz
inst/extdata/Groen_Supplemental_Table3c.csv.gz
inst/extdata/H322.csv
inst/extdata/HCC827-gef.csv
inst/extdata/HCC827.csv
inst/extdata/HCC827rep1.csv
inst/extdata/HCC827rep2.csv
inst/extdata/HCC827rep3.csv
inst/extdata/Hall2009_Table_S1.csv.gz
inst/extdata/Hall2009_Table_S4.csv.gz
inst/extdata/Hall2009_Table_S5.csv.gz
inst/extdata/Kozik_Dom_Data.csv
inst/extdata/Kozik_Dom_Data.xlsx
inst/extdata/MCF7.csv
inst/extdata/MarkersOrre2019.csv
inst/extdata/Nikolovski2012_SupplTable1.csv.gz
inst/extdata/Nikolovski2012_SupplTable2.csv.gz
inst/extdata/Nikolovski2012_SupplTable3.csv.gz
inst/extdata/OrganelleProfiles.TMT.HCMV.h120.csv.gz
inst/extdata/OrganelleProfiles.TMT.HCMV.h24.csv.gz
inst/extdata/OrganelleProfiles.TMT.HCMV.h48.csv.gz
inst/extdata/OrganelleProfiles.TMT.HCMV.h72.csv.gz
inst/extdata/OrganelleProfiles.TMT.HCMV.h96.csv.gz
inst/extdata/OrganelleProfiles.TMT.MOCK.h120.csv.gz
inst/extdata/OrganelleProfiles.TMT.MOCK.h24.csv.gz
inst/extdata/OrganelleProfiles.TMT.MOCK.h48.csv.gz
inst/extdata/OrganelleProfiles.TMT.MOCK.h72.csv.gz
inst/extdata/OrganelleProfiles.TMT.MOCK.h96.csv.gz
inst/extdata/Orre2019.csv
inst/extdata/PIIS0092867406003692.mmc2.csv.gz
inst/extdata/PIIS0092867406003692.mmc3.csv.gz
inst/extdata/PIIS0092867406003692.mmc4-highDensity.csv.gz
inst/extdata/PIIS0092867406003692.mmc4-lowDensity.csv.gz
inst/extdata/PIIS0092867406003692.mmc5-highDensity.csv.gz
inst/extdata/PIIS0092867406003692.mmc5-lowDensity.csv.gz
inst/extdata/PIIS0092867406003692.mmc6-localizations.csv.gz
inst/extdata/PIIS0092867406003692.mmc6-refinedLoc.csv.gz
inst/extdata/Protein_list.txt
inst/extdata/README
inst/extdata/Regrouped_MS2_full.csv.gz
inst/extdata/Regrouped_MS3_rep1_full.csv.gz
inst/extdata/Regrouped_MS3_rep2_inj2_full.csv.gz
inst/extdata/Shin2019ExpA1_RAWData.csv
inst/extdata/Shin2019ExpA2_RAWData.csv
inst/extdata/Shin2019ExpA3_RAWData.csv
inst/extdata/Shin2019ExpB1_RAWData.csv
inst/extdata/Shin2019ExpB2_RAWData.csv
inst/extdata/Shin2019ExpB3_RAWData.csv
inst/extdata/Shin2019ExpC1_RAWData.csv
inst/extdata/Shin2019ExpC2_RAWData.csv
inst/extdata/Shin2019ExpC3_RAWData.csv
inst/extdata/Shin2019newMarkers.csv
inst/extdata/Supplementary_Data_1_yeast2018.csv.gz
inst/extdata/TL123_complete.csv
inst/extdata/TanFlyMineFiltered.csv.gz
inst/extdata/TanFlyMineUnfiltered.csv.gz
inst/extdata/ToxoLOPIT_pData.csv
inst/extdata/U251.csv
inst/extdata/andy2011_Experimental_Info.txt
inst/extdata/andy2011_ispy_results_proteins_stringent.csv.gz
inst/extdata/boostingMarkers.Rmd
inst/extdata/boostingMarkers.pdf
inst/extdata/bpw-gocc.rds
inst/extdata/bpw-pdres.rds
inst/extdata/bpw-svmopt.rds
inst/extdata/bpw-tlopt.rds
inst/extdata/breckels2015.rda
inst/extdata/courtland2020pepitdedata.csv
inst/extdata/dc-geladaki-2018.csv.gz
inst/extdata/elife-16950-supp9-v3.xlsx
inst/extdata/exprsFile.csv.gz
inst/extdata/fdataFile.csv.gz
inst/extdata/hl-geladaki-2018.csv.gz
inst/extdata/hlMAPresults20180521.rda
inst/extdata/hlMCMCresults20180521.rda
inst/extdata/hyperLOPIT-SIData-fraction-info.csv
inst/extdata/hyperLOPIT-SIData-info.csv.gz
inst/extdata/hyperLOPIT-SIData-ms2-rep1.csv.gz
inst/extdata/hyperLOPIT-SIData-ms3-rep1.csv.gz
inst/extdata/hyperLOPIT-SIData-ms3-rep12-intersect.csv.gz
inst/extdata/hyperLOPIT-SIData-ms3-rep2.csv.gz
inst/extdata/hyperLOPIT-SIData-ms3-rep3.csv.gz
inst/extdata/hyperLOPIT_U2OS_201702.csv
inst/extdata/journal.pbio.2004411.s003.tab3.csv
inst/extdata/journal.pbio.2004411.s003.tab4.csv
inst/extdata/krahmer2018PhosphoPcp.csv
inst/extdata/krahmer2018PhosphoPcp.xlsx
inst/extdata/krahmer2018PhosphoPcpFeature.csv
inst/extdata/krahmer2018pcp.csv
inst/extdata/krahmer2018pcp.txt
inst/extdata/krahmer2018pcp.xlsx
inst/extdata/krahmer2018pcpFeature.csv
inst/extdata/lopimsSyn1.csv
inst/extdata/lopimsSyn2.csv
inst/extdata/lopimsSyn2_0frags.csv
inst/extdata/lopims_markers.csv
inst/extdata/markersDunkley.rda
inst/extdata/markersE14.rda
inst/extdata/markersHuman.rda
inst/extdata/markersTan.rda
inst/extdata/mmc2.xlsx
inst/extdata/mmc3.csv
inst/extdata/pdataFile.csv.gz
inst/extdata/pmic_201000359_sm_Shallow.csv.gz
inst/extdata/pmic_201000359_sm_Steep.csv.gz
inst/extdata/pr2010988_si_003.xls
inst/extdata/pr800866n_si_004-rep1.csv.gz
inst/extdata/pr800866n_si_004-rep2.csv.gz
inst/extdata/pr800866n_si_004-rep3.csv.gz
inst/extdata/pr800866n_si_007.csv.gz
inst/extdata/protein-complex-markers.rda
inst/extdata/silacDynamicItzhakCtrl.csv
inst/extdata/silacDynamicItzhakEGF.csv
inst/extdata/tabdelimited._gHentss2F9k.txt.gz
inst/extdata/thp1/LPS_timecourse_3reps_PSMs_301018.csv.gz
inst/extdata/thp1/LPS_timecourse_allreps_with_stats.csv.gz
inst/extdata/thp1/LPS_timecourse_r1.csv.gz
inst/extdata/thp1/LPS_timecourse_r2.csv.gz
inst/extdata/thp1/LPS_timecourse_r3.csv.gz
inst/extdata/thp1/psm_lps_rep1_set1_2mv_161218.csv.gz
inst/extdata/thp1/psm_lps_rep1_set2_2mv_161218.csv.gz
inst/extdata/thp1/psm_lps_rep2_set1_2mv_161218.csv.gz
inst/extdata/thp1/psm_lps_rep2_set2_2mv_161218.csv.gz
inst/extdata/thp1/psm_lps_rep3_set1_2mv_161218.csv.gz
inst/extdata/thp1/psm_lps_rep3_set2_2mv_161218.csv.gz
inst/extdata/thp1/psm_unstim_rep1_set1_2mv_051218.csv.gz
inst/extdata/thp1/psm_unstim_rep1_set2_2mv_051218.csv.gz
inst/extdata/thp1/psm_unstim_rep2_set1_2mv_051218.csv.gz
inst/extdata/thp1/psm_unstim_rep2_set2_2mv_051218.csv.gz
inst/extdata/thp1/psm_unstim_rep3_set1_2mv_051218.csv.gz
inst/extdata/thp1/psm_unstim_rep3_set2_2mv_051218.csv.gz
inst/extdata/thp1/sampleNames_timecourse.csv.gz
inst/extdata/thp1/thp1_LOPIT_lps_protein_full.csv.gz
inst/extdata/thp1/thp1_LOPIT_lps_protein_r1.csv.gz
inst/extdata/thp1/thp1_LOPIT_lps_protein_r2.csv.gz
inst/extdata/thp1/thp1_LOPIT_lps_protein_r3.csv.gz
inst/extdata/thp1/thp1_LOPIT_unst_protein_full.csv.gz
inst/extdata/thp1/thp1_LOPIT_unst_protein_r1.csv.gz
inst/extdata/thp1/thp1_LOPIT_unst_protein_r2.csv.gz
inst/extdata/thp1/thp1_LOPIT_unst_protein_r3.csv.gz
inst/extdata/thp1/thp1_pdata_lps_full.csv.gz
inst/extdata/thp1/thp1_pdata_unst_full.csv.gz
inst/extdata/tl-res/dunkley-tl.rda
inst/extdata/tl-res/groen-tl.rda
inst/extdata/tl-res/hpa-tl.rda
inst/extdata/tl-res/human-tl.rda
inst/extdata/tl-res/mouse-tl.rda
inst/extdata/tl-res/tan-tl.rda
inst/extdata/tl-res/yloc-tl.rda
inst/extdata/yloc_mouse_seqId_selected_features.csv
inst/scripts/E14TG2a.R
inst/scripts/Makefile
inst/scripts/Shin2020.R
inst/scripts/Stekhoven2014.R
inst/scripts/ToxoLopit.R
inst/scripts/addTanIds.R
inst/scripts/andreyev2010.R
inst/scripts/andy2011.R
inst/scripts/at_chloro.R
inst/scripts/beltran2016.R
inst/scripts/courtland2020.R
inst/scripts/davies2018.R
inst/scripts/dunkley2006.R
inst/scripts/fabre2015.R
inst/scripts/foster2006.R
inst/scripts/geladaki2018.R
inst/scripts/groen2014.R
inst/scripts/hall2009.R
inst/scripts/havugimana2012.R
inst/scripts/hirst2018.R
inst/scripts/hyperLOPITU2OS2017.R
inst/scripts/hyperlopit2015.R
inst/scripts/hyperlopit2015psm.R
inst/scripts/itzhak2016.R
inst/scripts/itzhak2016dynamic.R
inst/scripts/itzhak2017.R
inst/scripts/kirkwood2013.R
inst/scripts/kozik2020.R
inst/scripts/krahmer2018pcp.R
inst/scripts/krahmer2018phosphopcp.R
inst/scripts/kristensen2012.R
inst/scripts/lopmissyn2.R
inst/scripts/moloney2023.R
inst/scripts/mulvey2015.R
inst/scripts/nikolovski2012.R
inst/scripts/nikolovski2014.R
inst/scripts/orre2019a431.R
inst/scripts/orre2019h322.R
inst/scripts/orre2019hcc827.R
inst/scripts/orre2019hcc827gef.R
inst/scripts/orre2019hcc827rep1.R
inst/scripts/orre2019hcc827rep2.R
inst/scripts/orre2019hcc827rep3.R
inst/scripts/orre2019mcf7.R
inst/scripts/orre2019u251.R
inst/scripts/protein-complex-markers.R
inst/scripts/rodriguez-pineiro2012.R
inst/scripts/runnall.sh
inst/scripts/tan2009.R
inst/scripts/thpLOPIT2021.R
inst/scripts/thpTimecourse2021.R
inst/scripts/trotter2010.R
inst/scripts/yeast2018.R
inst/scripts/ylocMouse.R
man/E14TG2a.Rd
man/Shin2020.Rd
man/ToxoLopit.Rd
man/andreyev2010.Rd
man/andy2011.Rd
man/at_chloro.Rd
man/baers2018.Rd
man/beltran2016.Rd
man/courtland2020.rd
man/davies2018.rd
man/dunkley2006.Rd
man/fabre2015.Rd
man/foster2006.Rd
man/groen2014.Rd
man/hall2009.Rd
man/havugimana2012.Rd
man/hirst2018.Rd
man/hyperLOPIT2015.Rd
man/hyperLOPITU2OS2017.Rd
man/itzhak2016stcSILAC.Rd
man/itzhak2017.Rd
man/itzhak2017dynamic.rd
man/kirkwood2013.Rd
man/kozik2020.rd
man/krahmer2018pcp.Rd
man/kristensen2012.Rd
man/lopimsSyn2.Rd
man/moloney2023.Rd
man/mulvey2015.Rd
man/nikolovski2012.Rd
man/nikolovski2014.Rd
man/orre2019.rd
man/pRolocdata.Rd
man/pRolocmetadata.Rd
man/rodriguez2012r1.Rd
man/stekhoven2014.Rd
man/tan2009.Rd
man/thpLOPIT2021.Rd
man/thpTimecourse2021.Rd
man/trotter2010.Rd
man/yeast.Rd
tests/testthat.R
tests/testthat/test_data.R
