Files in avucoh/nPOD
What the Package Does (One Line, Title Case)
.Rbuildignore
.Rhistory
.gitignore
DESCRIPTION
NAMESPACE
R/data.R
R/nPOD_DIVE.R
data/cdata.rda
data/cdatabin.rda
data/cordata.rda
data/hdata.rda
data/hpcg.rda
data/matrix_metadata.rda
data/metadata.rda
data/metadata_ext.rda
data/metadata_map.rda
data/ndata.rda
data/npodX.rda
data/npodgraph.rda
data/px1_t.rda
data/px2_t.rda
data/srcnetwork.rda
data/visNetD.rda
data/xm2_t.rda
data/xm_t.rda
inst/Dockerfile
inst/app/.Rhistory
inst/app/appdata/DemoCohort.csv
inst/app/appdata/divid.csv
inst/app/appdata/divid_coded.csv
inst/app/appdata/divid_uncoded.csv
inst/app/appdata/examplecohort2020.csv
inst/app/appdata/mixed.csv
inst/app/appdata/sample_ID_list.txt
inst/app/appdata/t1dbase.txt
inst/app/appdata/xm_t.csv
inst/app/global.R
inst/app/server.R
inst/app/shiny_bookmarks/5a41108047b2596e/input.rds
inst/app/shiny_bookmarks/5a41108047b2596e/values.rds
inst/app/shiny_bookmarks/7013cb8c9ab03ae5/input.rds
inst/app/shiny_bookmarks/7013cb8c9ab03ae5/values.rds
inst/app/shiny_bookmarks/af5733e26e5a2bee/input.rds
inst/app/shiny_bookmarks/af5733e26e5a2bee/values.rds
inst/app/shiny_bookmarks/c8c0c013faa66980/input.rds
inst/app/shiny_bookmarks/c8c0c013faa66980/values.rds
inst/app/ui.R
inst/app/ui_home.R
inst/app/www/cellpack.json
inst/app/www/content/feature1.Rmd
inst/app/www/content/feature2.Rmd
inst/app/www/content/feature3.Rmd
inst/app/www/content/feature4.Rmd
inst/app/www/custom.css
inst/app/www/demo/cohort_exchange.txt
inst/app/www/demo/data_exploration.txt
inst/app/www/demo/demoCohort.js
inst/app/www/demo/demoMatrix.js
inst/app/www/help/browse_data.Rmd
inst/app/www/help/cohort_exchange.Rmd
inst/app/www/help/matching_methods.Rmd
inst/app/www/intro.min.js
inst/app/www/introjs.min.css
inst/app/www/nPOD_logo.jpeg
inst/data-raw/.Rhistory
inst/data-raw/core/.~lock.HiResHLAclean.tsv#
inst/data-raw/core/AutoAb.tsv
inst/data-raw/core/Demographics.tsv
inst/data-raw/core/DiabetesInfo.tsv
inst/data-raw/core/HiResHLAclean.tsv
inst/data-raw/core/HiResHLAclean_processed.tsv
inst/data-raw/core/PMID23232891_Campbell-Thompson-2012.csv
inst/data-raw/core/PancreasWeights.csv
inst/data-raw/core/core.R
inst/data-raw/core/pancreas_weight_only.csv
inst/data-raw/core/riskII_ref.tsv
inst/data-raw/core/riskI_ref.tsv
inst/data-raw/datasets/.RData
inst/data-raw/datasets/.~lock.Metadata.tsv#
inst/data-raw/datasets/.~lock.Methods.tsv#
inst/data-raw/datasets/Core_Autoantibody.tsv
inst/data-raw/datasets/Core_Demographics.tsv
inst/data-raw/datasets/Core_DiabetesInfo.tsv
inst/data-raw/datasets/Core_HLA_phased.tsv
inst/data-raw/datasets/Core_RIN.tsv
inst/data-raw/datasets/Core_Serology.tsv
inst/data-raw/datasets/MH/.Rhistory
inst/data-raw/datasets/PMID20062967_1_Gianani-2010.tsv
inst/data-raw/datasets/PMID22213807_1_Coppieters-2012.tsv
inst/data-raw/datasets/PMID22923498_1_Yip-2012.tsv
inst/data-raw/datasets/PMID23064357_1_Richardson-2012.tsv
inst/data-raw/datasets/PMID23139348_1_Korpos-2012.tsv
inst/data-raw/datasets/PMID23232891_1_Campbell-Thompson-2012.tsv
inst/data-raw/datasets/PMID23904478_1_Chen-2013.tsv
inst/data-raw/datasets/PMID23920110_1_Kavishwar-2013.tsv
inst/data-raw/datasets/PMID24225943_1_Engin-2013.tsv
inst/data-raw/datasets/PMID24264405_1_Yip-2013.tsv
inst/data-raw/datasets/PMID24498006_1_Ye-2014.tsv
inst/data-raw/datasets/PMID24514745_1_Engin-2014.tsv
inst/data-raw/datasets/PMID24947367_1_RodriguezCalvo-2014.tsv
inst/data-raw/datasets/PMID25532042_1_Grzesik-2014.tsv
inst/data-raw/datasets/PMID25687234_1_Reddy-2015.tsv
inst/data-raw/datasets/PMID26055066_1_Taniguchi-2015.tsv
inst/data-raw/datasets/PMID26076035_1_vanderMeulen-2015.tsv
inst/data-raw/datasets/PMID26358584_1_CampbellThompson15.tsv
inst/data-raw/datasets/PMID26581594_1_CampbellThompson-2016.tsv
inst/data-raw/datasets/PMID26581594_2_CampbellThompson-2016.tsv
inst/data-raw/datasets/PMID26829442_1_Diedisheim-16.tsv
inst/data-raw/datasets/PMID26935967_1_Liu-2016.tsv
inst/data-raw/datasets/PMID26983959_1_Kodama-2016.tsv
inst/data-raw/datasets/PMID27284108_1_Phelps-2016.tsv
inst/data-raw/datasets/PMID27506584_1_Richardson-2016.tsv
inst/data-raw/datasets/PMID27813705_1_Moin-2016.tsv
inst/data-raw/datasets/PMID27942583_1_Seay-2016.tsv
inst/data-raw/datasets/PMID28094469_1_Kirk-2017.tsv
inst/data-raw/datasets/PMID28137793_1_RodriguezCalvo-2017.tsv
inst/data-raw/datasets/PMID28154952_1_Martin-2017.tsv
inst/data-raw/datasets/PMID28323930_1_Lam-2017.tsv
inst/data-raw/datasets/PMID28325643_1_Anquetil-2017.tsv
inst/data-raw/datasets/PMID28380379_1_Bonner-Weir-2019.csv
inst/data-raw/datasets/PMID28428323_1_Jackson-2017.tsv
inst/data-raw/datasets/PMID28742858_1_Thivolet-2017.tsv
inst/data-raw/datasets/PMID28761107_1_Sebastiani-2017.tsv
inst/data-raw/datasets/PMID28761107_2_Sebastiani-2017.tsv
inst/data-raw/datasets/PMID28877242_1_Nyalwidhe-2017.tsv
inst/data-raw/datasets/PMID28877460_1_Wasserfall-2017.tsv
inst/data-raw/datasets/PMID28878130_1_Levet-2017.tsv
inst/data-raw/datasets/PMID29128936_1_Kusmartseva-2017.tsv
inst/data-raw/datasets/PMID29326366_1_Lam-2018.tsv
inst/data-raw/datasets/PMID29337308_1_Abedini-2018.tsv
inst/data-raw/datasets/PMID29352311_1_BonnetSerrano-2018.tsv
inst/data-raw/datasets/PMID29415062_1_Simeonovic-2018.tsv
inst/data-raw/datasets/PMID29429978_1_Culina-2018.tsv
inst/data-raw/datasets/PMID29589071_1_Reddy-2018.tsv
inst/data-raw/datasets/PMID29671030_1_Holm-2018.tsv
inst/data-raw/datasets/PMID29754954_1_Lu-2018.tsv
inst/data-raw/datasets/PMID29771178_1_Canzano-2018.tsv
inst/data-raw/datasets/PMID29792697_1_Heller-2018.tsv
inst/data-raw/datasets/PMID30078552_1_GonzalezDuque-2018.tsv
inst/data-raw/datasets/PMID30150306_1_Horwitz-2018.tsv
inst/data-raw/datasets/PMID30203067_1_Capua-2018.tsv
inst/data-raw/datasets/PMID30232284_1_Vecchio-2018.tsv
inst/data-raw/datasets/PMID30552110_1_Lam-2019.tsv
inst/data-raw/datasets/PMID30713109_1_Damond-2019.tsv
inst/data-raw/datasets/PMID30713110_1_Wang-2019.tsv
inst/data-raw/datasets/PMID30759032_1_Teitelman-19.tsv
inst/data-raw/datasets/PMID30799288_1_Thompson-2019.tsv
inst/data-raw/datasets/PMID31486854_1_Postigo-Fernandez-2019.tsv
inst/data-raw/datasets/PMID31486854_2_Postigo-Fernandez-2019.tsv
inst/data-raw/excluded/Fewsamples/PMID26858360_Leete-2016.tsv
inst/data-raw/excluded/MetadataOnly/PMID22069254_Coppietiers2011.tsv
inst/data-raw/excluded/MetadataOnly/PMID22210319_Sarkar-2012.tsv
inst/data-raw/excluded/MetadataOnly/PMID22699564_Marhfour-2012.tsv
inst/data-raw/excluded/MetadataOnly/PMID22745242_Gregg-2012.tsv
inst/data-raw/excluded/MetadataOnly/PMID23904478_Chen-2013.tsv
inst/data-raw/excluded/MetadataOnly/PMID24264405_Yip-2013.csv
inst/data-raw/excluded/MetadataOnly/PMID24677718_Bogdani-2014.tsv
inst/data-raw/excluded/MetadataOnly/PMID25077543_Piran-2014.tsv
inst/data-raw/excluded/MetadataOnly/PMID25226365_Subauste-2014.tsv
inst/data-raw/excluded/MetadataOnly/PMID25422108_Krogvold-2014.tsv
inst/data-raw/excluded/MetadataOnly/PMID25532042_Grzesik-2014.csv
inst/data-raw/excluded/MetadataOnly/PMID25576800_Harms-2015.tsv
inst/data-raw/excluded/MetadataOnly/PMID26950362_Helman-2016.tsv
inst/data-raw/excluded/MetadataOnly/PMID27300574_Moin-2016.tsv
inst/data-raw/excluded/MetadataOnly/PMID27798614_Babon-2016.tsv
inst/data-raw/excluded/MetadataOnly/PMID27809303_Piran-2016.tsv
inst/data-raw/excluded/MetadataOnly/PMID27813705_Moin-2016.csv
inst/data-raw/excluded/MetadataOnly/PMID28119693_Graves-2016.tsv
inst/data-raw/excluded/MetadataOnly/PMID28137793_RodriguezCalvo-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID28213757_Willcox-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID28380379_AguayoMazzucato-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID28380380_vanderMeulen-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID28581443_Waqas-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID28614797_Rodnoi-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID28679961_Schludi-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID28782056_Moin-2017.tsv
inst/data-raw/excluded/MetadataOnly/PMID29506054_Aslamy-2018.tsv
inst/data-raw/excluded/MetadataOnly/PMID30338340_Leslie-2019.tsv
inst/data-raw/metadata-table/.~lock.Metadata.tsv#
inst/data-raw/metadata-table/Metadata.tsv
inst/data-raw/metadata-table/Methods.tsv
inst/data-raw/process/.~lock.curation_process.tsv#
inst/data-raw/process/Core/A5_phased_supplement.tsv
inst/data-raw/process/Core/A_C_B_DRB1_DQB1.tsv
inst/data-raw/process/Core/HLA_diff.tsv
inst/data-raw/process/Core/HLA_diff_formatted.tsv
inst/data-raw/process/Core/HiResHLAclean.tsv
inst/data-raw/process/Core/HiResHLAclean_ref.tsv
inst/data-raw/process/Core/Histopathology.tsv
inst/data-raw/process/Core/histology.R
inst/data-raw/process/Core/phaseHLA.R
inst/data-raw/process/Core/phaseHLA_fun.R
inst/data-raw/process/Core/phaseHLA_supplement.R
inst/data-raw/process/Core/xC_phased_supplement.tsv
inst/data-raw/process/Core_Autoantibody/process.R
inst/data-raw/process/Core_Demographics/Demographics_2019-12-24.tsv
inst/data-raw/process/Core_DiabetesInfo/process.R
inst/data-raw/process/Core_HLA/HiResHLA_2019-12-24.tsv
inst/data-raw/process/Core_HLA/process.R
inst/data-raw/process/Core_RIN/RNA_RIN.tsv
inst/data-raw/process/Core_Serology/Serology.tsv
inst/data-raw/process/Core_Serology/process.R
inst/data-raw/process/PMID20062967_Gianani-2010/table1.pdf
inst/data-raw/process/PMID22213807_Coppieters-2012/jem_20111187_sm.pdf
inst/data-raw/process/PMID22213807_Coppieters-2012/process.R
inst/data-raw/process/PMID22923498_Yip-2012/Fathman nPOD data-PMID 22923498.xlsx
inst/data-raw/process/PMID22923498_Yip-2012/process.R
inst/data-raw/process/PMID23064357_Richardson-2012/process.R
inst/data-raw/process/PMID23139348_Korpos-2012/DB120432SupplementaryData_2-3.pdf
inst/data-raw/process/PMID23139348_Korpos-2012/process.R
inst/data-raw/process/PMID23904478_Chen-2013/figs5.png
inst/data-raw/process/PMID23904478_Chen-2013/pnas.1312911110fig06.jpg
inst/data-raw/process/PMID23904478_Chen-2013/text.png
inst/data-raw/process/PMID23920110_Kavishwar-2013/process.R
inst/data-raw/process/PMID24225943_Engin-2013/nPOD samples.xlsx
inst/data-raw/process/PMID24225943_Engin-2013/process.R
inst/data-raw/process/PMID24264405_Yip-2013/4208fig4.jpg
inst/data-raw/process/PMID24264405_Yip-2013/4208tbl1.jpg
inst/data-raw/process/PMID24264405_Yip-2013/fig4.txt
inst/data-raw/process/PMID24264405_Yip-2013/tbl1.txt
inst/data-raw/process/PMID24498006_Ye-2014/.~lock.pone.0086985.s003.docx#
inst/data-raw/process/PMID24498006_Ye-2014/pone.0086985.s003.docx
inst/data-raw/process/PMID24498006_Ye-2014/process.R
inst/data-raw/process/PMID24514745_Engin-2014/nPOD samples.xlsx
inst/data-raw/process/PMID24514745_Engin-2014/process.R
inst/data-raw/process/PMID25532042_Grzesik-2014/jc-14-3630.pdf
inst/data-raw/process/PMID25687234_Reddy-2015/process.R
inst/data-raw/process/PMID26055066_Taniguchi-2015/tab1.png
inst/data-raw/process/PMID26055066_Taniguchi-2015/tab2.png
inst/data-raw/process/PMID26581594_CampbellThompson-2016/process.R
inst/data-raw/process/PMID26935967_Liu-2016/Liu-2016_TableS1.tsv
inst/data-raw/process/PMID26935967_Liu-2016/process.R
inst/data-raw/process/PMID26983959_Kodama-2016/process.R
inst/data-raw/process/PMID27284108_Phelps-2016/DB160180SupplementaryData.pdf
inst/data-raw/process/PMID27506584_Richardson-2016/125_2016_4067_Fig3_HTML.jpg
inst/data-raw/process/PMID27506584_Richardson-2016/125_2016_4067_Fig4_HTML.jpg
inst/data-raw/process/PMID27813705_Moin-2016/process.R
inst/data-raw/process/PMID28137793_RodriguezCalvo-2017/DB161343SupplementaryData_SFig3.pdf
inst/data-raw/process/PMID28323930_Lam-2017/jc.2016-3806.st1.xlsx
inst/data-raw/process/PMID28380379_Bonner-Weir-2017/.~lock.p53BP1 igfr human.xlsx#
inst/data-raw/process/PMID28380379_Bonner-Weir-2017/p53BP1 igfr human.xlsx
inst/data-raw/process/PMID28742858_Thivolet-2017/process.R
inst/data-raw/process/PMID28761107_Sebastiani-2017/miRNA_profiling_nPOD_samples.xlsx
inst/data-raw/process/PMID28761107_Sebastiani-2017/process.R
inst/data-raw/process/PMID28877242_Nyalwidhe-2017/Nyalwidhe-2017_TableS4.xlsx
inst/data-raw/process/PMID28877242_Nyalwidhe-2017/Nyalwidhe-2017_TableS4_A.tsv
inst/data-raw/process/PMID28877242_Nyalwidhe-2017/Nyalwidhe-2017_TableS4_B.tsv
inst/data-raw/process/PMID28878130_Levet-2017/.~lock.18-07-03 compilation CD3 CD68 Env03 nPOD.xlsx#
inst/data-raw/process/PMID28878130_Levet-2017/18-07-03 compilation CD3 CD68 Env03 nPOD.xlsx
inst/data-raw/process/PMID28878130_Levet-2017/process.R
inst/data-raw/process/PMID29326366_Lam-2018/Lam et al nPOD Islet Cell Suppl Tables 12 16 2017 CJL.xlsx
inst/data-raw/process/PMID29337308_Abedini-2018/jci-128-85210-s001_stab2.pdf
inst/data-raw/process/PMID29415062_Simeonovic-2018/pone.0191360.s006.xlsx
inst/data-raw/process/PMID29415062_Simeonovic-2018/process.R
inst/data-raw/process/PMID29589071_Reddy-2018/125_2018_4600_MOESM1_ESM.pdf
inst/data-raw/process/PMID29671030_Holm-2018/PMID29671030_Holm18.tsv
inst/data-raw/process/PMID29671030_Holm-2018/process.R
inst/data-raw/process/PMID29754954_Lu-2018/20200121_npod_fig2_data.xlsx
inst/data-raw/process/PMID29754954_Lu-2018/process.R
inst/data-raw/process/PMID29771178_Canzano-2018/DS_10.1369_0022155418778546.pdf
inst/data-raw/process/PMID30552110_Lam-2019/DB180305SupplementaryData_Table5.pdf
inst/data-raw/process/PMID30552110_Lam-2019/DB180305SupplementaryData_Table6.pdf
inst/data-raw/process/PMID30552110_Lam-2019/DB180305SupplementaryData_Table7.pdf
inst/data-raw/process/PMID30552110_Lam-2019/DB180305SupplementaryData_manual_extraction.xlsx
inst/data-raw/process/PMID30552110_Lam-2019/process.R
inst/data-raw/process/PMID30713109_Damond-2019/All_Image.csv
inst/data-raw/process/PMID30713109_Damond-2019/Metadata.csv
inst/data-raw/process/PMID30713109_Damond-2019/process.R
inst/data-raw/process/PMID30713109_Damond-2019/process.png
inst/data-raw/process/PMID30713110_Wang-2019/.~lock.NIHMS1518414-supplement-Table_s6.xlsx#
inst/data-raw/process/PMID30713110_Wang-2019/NIHMS1518414-supplement-Table_s6.xlsx
inst/data-raw/process/PMID30713110_Wang-2019/process.R
inst/data-raw/process/PMID30713110_Wang-2019/process.png
inst/data-raw/process/PMID31486854_Postigo-Fernandez-2019/Human LNSCs gene expression datasheet.xlsx
inst/data-raw/process/PMID31486854_Postigo-Fernandez-2019/MHCII & PD-L1.xlsx
inst/data-raw/process/PMID31486854_Postigo-Fernandez-2019/Relative frequency of SCs.xlsx
inst/data-raw/process/PMID31486854_Postigo-Fernandez-2019/process.R
inst/data-raw/process/curation_process.tsv
inst/make.yml
inst/shiny-server.conf
nPOD.Rproj
