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philipmorrisintl · Aug 27, 2019 · fc805ec · fc805ec
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diff --git a/.gitattributes b/.gitattributes
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+**/*.rda filter=lfs diff=lfs merge=lfs -text
+**/*.rds filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitignore b/.gitignore
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+# .gitignore for public github
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
+rsconnect/
+
+# Do not include external data files
+DATA/EXTERNAL/
+
+# Ignore result folder and Rmd output folder
+REPORT/
+SCRIPTS/P15038_APOE_P2_MultiOmicsManuscript_files/
+
+TMP/
+
+README.html
diff --git a/DATA/CITATION b/DATA/CITATION
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+CITATION/REFERENCE
+
+HCOP_ORTHOLOGY_TABLE.rda
+https://www.genenames.org/help/hcop/
+Wright MW, Eyre TA, Lush MJ, Povey S and Bruford EA. HCOP: The HGNC Comparison of Orthology Predictions Search Tool. Mamm Genome. 2005 Nov; 16(11):827-828. PMID:16284797
+Eyre TA, Wright MW, Lush MJ and Bruford EA. HCOP: a searchable database of human orthology predictions. Brief Bioinform. 2007 Jan;8(1):2-5. PMID:16951416
+Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. genenames.org: the HGNC resources in 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D519-9. PMID: 20929869
+
diff --git a/DATA/DATA-P15038-S186400_APOE_P2_Lung_Mm_LIPSG.rda b/DATA/DATA-P15038-S186400_APOE_P2_Lung_Mm_LIPSG.rda
diff --git a/DATA/DATA-Tissue_APOE_P2_Lung_Ms_METABOLOMICS.rda b/DATA/DATA-Tissue_APOE_P2_Lung_Ms_METABOLOMICS.rda
diff --git a/DATA/DATA-_APOE_P2_Lung_Mm_PEX.rda b/DATA/DATA-_APOE_P2_Lung_Mm_PEX.rda
diff --git a/DATA/DATA_P15038-S185500_APOE_P2_Lung_Mm_MIRNA.rda b/DATA/DATA_P15038-S185500_APOE_P2_Lung_Mm_MIRNA.rda
diff --git a/DATA/DATA_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda b/DATA/DATA_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda
diff --git a/DATA/GeneIDTable.Mm.rda b/DATA/GeneIDTable.Mm.rda
diff --git a/DATA/HCOP_ORTHOLOGY_TABLE.rda b/DATA/HCOP_ORTHOLOGY_TABLE.rda
diff --git a/DATA/HomologTable.rda b/DATA/HomologTable.rda
diff --git a/DATA/IDMAP-P15038-S186400_APOE_P2_Lung_Mm_LIPSG.rda b/DATA/IDMAP-P15038-S186400_APOE_P2_Lung_Mm_LIPSG.rda
diff --git a/DATA/IDMAP-Tissue_APOE_P2_Lung_Ms_METABOLOMICS.rda b/DATA/IDMAP-Tissue_APOE_P2_Lung_Ms_METABOLOMICS.rda
diff --git a/DATA/IDMAP-_APOE_P2_Lung_Mm_PEX.rda b/DATA/IDMAP-_APOE_P2_Lung_Mm_PEX.rda
diff --git a/DATA/IDMAP_P15038-S185500_APOE_P2_Lung_Mm_MIRNA.rda b/DATA/IDMAP_P15038-S185500_APOE_P2_Lung_Mm_MIRNA.rda
diff --git a/DATA/IDMAP_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda b/DATA/IDMAP_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda
diff --git a/DATA/LICENSE b/DATA/LICENSE
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+This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
+
+License applies to provided data files:
+IDMAP_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda   
+NPALIST_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda
+DATA-_APOE_P2_Lung_Mm_PEX.rda                  
+IDMAP-P15038-S186400_APOE_P2_Lung_Mm_LIPSG.rda  
+P15038_APOE_P2_BALF_cells.rda
+DATA_P15038-S185500_APOE_P2_Lung_Mm_MIRNA.rda  
+IDMAP-Tissue_APOE_P2_Lung_Ms_METABOLOMICS.rda   
+P15038_APOE_P2_Exposure.rda
+DATA_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda   
+P15038_LungManuscript_LipidMappingTable3_bt.csv
+DATA-P15038-S186400_APOE_P2_Lung_Mm_LIPSG.rda  
+IDMAP-_APOE_P2_Lung_Mm_PEX.rda                  
+DATA-Tissue_APOE_P2_Lung_Ms_METABOLOMICS.rda   
+IDMAP_P15038-S185500_APOE_P2_Lung_Mm_MIRNA.rda  
diff --git a/DATA/MapApprovedSynonyms.Hs.2014-11-27.rda b/DATA/MapApprovedSynonyms.Hs.2014-11-27.rda
diff --git a/DATA/MapApprovedSynonyms.Mm.2014-11-27.rda b/DATA/MapApprovedSynonyms.Mm.2014-11-27.rda
diff --git a/DATA/NPALIST_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda b/DATA/NPALIST_P15038-S185500_APOE_P2_Lung_Mm_MRNA.rda
diff --git a/DATA/P15038_APOE_P2_BALF_cells.rda b/DATA/P15038_APOE_P2_BALF_cells.rda
diff --git a/DATA/P15038_APOE_P2_Exposure.rda b/DATA/P15038_APOE_P2_Exposure.rda
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