├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── biocarta.R ├── data.R └── package.R ├── _pkgdown.yml ├── data ├── BC2ENTREZ.RData ├── BIOCARTA_PATHWAYS.RData ├── PATHWAY2BC.RData ├── PATHWAY2ENTREZ.RData ├── PATHWAY2MSIGDB.RData └── datalist ├── docs ├── 404.html ├── LICENSE-text.html ├── articles │ ├── BioCartaImage.html │ ├── BioCartaImage_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── image │ ├── H_cdc25Pathway.gif │ ├── H_gsk3Pathway.gif │ ├── h_41BBPathway.gif │ ├── h_AnthraxPathway.gif │ ├── h_CaCaMPathway.gif │ ├── h_DNAfragmentPathway.gif │ ├── h_EfpPathway.gif │ ├── h_ErbB3Pathway.gif │ ├── h_FlumazenilPathway.gif │ ├── h_LDLpathway.gif │ ├── h_LairPathway.gif │ ├── h_Lis1Pathway.gif │ ├── h_PDZsPathway.gif │ ├── h_PPARgPathway.gif │ ├── h_PparaPathway.gif │ ├── h_RNApol3Pathway.gif │ ├── h_SARSpathway.gif │ ├── h_WNVpathway.gif │ ├── h_aMANpathway.gif │ ├── h_ace2Pathway.gif │ ├── h_acetaminophenPathway.gif │ ├── h_achPathway.gif │ ├── h_acrPathway.gif │ ├── h_actinYPathway.gif │ ├── h_agpcrPathway.gif │ ├── h_agrPathway.gif │ ├── h_ahspPathway.gif │ ├── h_aifPathway.gif │ ├── h_akap13Pathway.gif │ ├── h_akap95Pathway.gif │ ├── h_akapcentrosomePathway.gif │ ├── h_aktPathway.gif │ ├── h_alkPathway.gif │ ├── h_alternativePathway.gif │ ├── h_amiPathway.gif │ ├── h_antisensePathway.gif │ ├── h_appPathway.gif │ ├── h_arapPathway.gif │ ├── h_arenrf2Pathway.gif │ ├── h_arfPathway.gif │ ├── h_argininecPathway.gif │ ├── h_asbcellPathway.gif │ ├── h_at1rPathway.gif │ ├── h_atmPathway.gif │ ├── h_atrbrcaPathway.gif │ ├── h_bArr-mapkPathway.gif │ ├── h_bArrestin-srcPathway.gif │ ├── h_bArrestinPathway.gif │ ├── h_badPathway.gif │ ├── h_bard1Pathway.gif │ ├── h_bbcellPathway.gif │ ├── h_bcellsurvivalPathway.gif │ ├── h_bcrPathway.gif │ ├── h_bcrmolecule.gif │ ├── h_biopeptidesPathway.gif │ ├── h_blymphocytePathway.gif │ ├── h_botulinPathway.gif │ ├── h_btg2Pathway.gif │ ├── h_calcineurinPathway.gif │ ├── h_cardiacEGFPathway.gif │ ├── h_carm-erPathway.gif │ ├── h_carm1Pathway.gif │ ├── h_caspasePathway.gif │ ├── h_cb1rPathway.gif │ ├── h_cblPathway.gif │ ├── h_ccr3Pathway.gif │ ├── h_ccr5Pathway.gif │ ├── h_cd40Pathway.gif │ ├── h_cdc42racPathway.gif │ ├── h_cdk5Pathway.gif │ ├── h_cdmacPathway.gif │ ├── h_cell2cellPathway.gif │ ├── h_cellcyclePathway.gif │ ├── h_ceramidePathway.gif │ ├── h_cftrPathway.gif │ ├── h_chemicalPathway.gif │ ├── h_chrebpPathway.gif │ ├── h_circadianPathway.gif │ ├── h_ck1Pathway.gif │ ├── h_classicPathway.gif │ ├── h_compPathway.gif │ ├── h_cpsfPathway.gif │ ├── h_cptPathway.gif │ ├── h_crebPathway.gif │ ├── h_cremPathway.gif │ ├── h_cskPathway.gif │ ├── h_ctbp1Pathway.gif │ ├── h_ctcfPathway.gif │ ├── h_ctlPathway.gif │ ├── h_ctla4Pathway.gif │ ├── h_cxcr4Pathway.gif │ ├── h_cytokinePathway.gif │ ├── h_d4gdiPathway.gif │ ├── h_dbpbPathway.gif │ ├── h_dcPathway.gif │ ├── h_deathPathway.gif │ ├── h_dicerPathway.gif │ ├── h_dreamPathway.gif │ ├── h_dspPathway.gif │ ├── h_ecmPathway.gif │ ├── h_edg1Pathway.gif │ ├── h_eea1Pathway.gif │ ├── h_egfPathway.gif │ ├── h_egfr_smrtePathway.gif │ ├── h_eicosanoidPathway.gif │ ├── h_eif2Pathway.gif │ ├── h_eif4Pathway.gif │ ├── h_eifPathway.gif │ ├── h_eosinophilsPathway.gif │ ├── h_ephA4Pathway.gif │ ├── h_epoPathway.gif │ ├── h_eponfkbPathway.gif │ ├── h_eradPathway.gif │ ├── h_erbb4Pathway.gif │ ├── h_erk5Pathway.gif │ ├── h_erkPathway.gif │ ├── h_erythPathway.gif │ ├── h_etcPathway.gif │ ├── h_etsPathway.gif │ ├── h_extrinsicPathway.gif │ ├── h_fasPathway.gif │ ├── h_fbw7Pathway.gif │ ├── h_fcer1Pathway.gif │ ├── h_fibrinolysisPathway.gif │ ├── h_fmlpPathway.gif │ ├── h_fosbPathway.gif │ ├── h_freePathway.gif │ ├── h_fxrPathway.gif │ ├── h_g1Pathway.gif │ ├── h_g1pPathway.gif │ ├── h_g2Pathway.gif │ ├── h_gabaPathway.gif │ ├── h_gata3Pathway.gif │ ├── h_gcrpathway.gif │ ├── h_ghPathway.gif │ ├── h_ghrelinPathway.gif │ ├── h_gleevecPathway.gif │ ├── h_glycolysisPathway.gif │ ├── h_gpcrPathway.gif │ ├── h_granulocytesPathway.gif │ ├── h_gsPathway.gif │ ├── h_hSWI-SNFpathway.gif │ ├── h_hbxPathway.gif │ ├── h_hcmvPathway.gif │ ├── h_hdacPathway.gif │ ├── h_her2Pathway.gif │ ├── h_hesPathway.gif │ ├── h_hifPathway.gif │ ├── h_hivnefPathway.gif │ ├── h_hopPathway.gif │ ├── h_hsp27Pathway.gif │ ├── h_huntingtonPathway.gif │ ├── h_ifnaPathway.gif │ ├── h_ifngPathway.gif │ ├── h_igf1Pathway.gif │ ├── h_igf1mtorPathway.gif │ ├── h_igf1rPathway.gif │ ├── h_il10Pathway.gif │ ├── h_il12Pathway.gif │ ├── h_il17Pathway.gif │ ├── h_il18Pathway.gif │ ├── h_il1rPathway.gif │ ├── h_il22bpPathway.gif │ ├── h_il2Pathway.gif │ ├── h_il2rbPathway.gif │ ├── h_il3Pathway.gif │ ├── h_il4Pathway.gif │ ├── h_il5Pathway.gif │ ├── h_il6Pathway.gif │ ├── h_il7Pathway.gif │ ├── h_inflamPathway.gif │ ├── h_insulinPathway.gif │ ├── h_integrinPathway.gif │ ├── h_intrinsicPathway.gif │ ├── h_ionPathway.gif │ ├── h_iresPathway.gif │ ├── h_keratinocytePathway.gif │ ├── h_lectinPathway.gif │ ├── h_leptinPathway.gif │ ├── h_longevityPathway.gif │ ├── h_lymPathway.gif │ ├── h_lymphocytePathway.gif │ ├── h_mCalpainPathway.gif │ ├── h_mPRPathway.gif │ ├── h_malPathway.gif │ ├── h_malatePathway.gif │ ├── h_malatexPathway.gif │ ├── h_mapkPathway.gif │ ├── h_mcmPathway.gif │ ├── h_mef2dPathway.gif │ ├── h_melanocytePathway.gif │ ├── h_metPathway.gif │ ├── h_methioninePathway.gif │ ├── h_mhcPathway.gif │ ├── h_mitochondriaPathway.gif │ ├── h_mitrPathway.gif │ ├── h_monocytePathway.gif │ ├── h_mrpPathway.gif │ ├── h_mspPathway.gif │ ├── h_mta3Pathway.gif │ ├── h_mtorPathway.gif │ ├── h_myosinPathway.gif │ ├── h_ndkDynaminPathway.gif │ ├── h_neutrophilPathway.gif │ ├── h_nfatPathway.gif │ ├── h_nfkbPathway.gif │ ├── h_ngfPathway.gif │ ├── h_nkcellsPathway.gif │ ├── h_nktPathway.gif │ ├── h_no1Pathway.gif │ ├── h_no2il12Pathway.gif │ ├── h_nos1Pathway.gif │ ├── h_notchPathway.gif │ ├── h_npcPathway.gif │ ├── h_npp1Pathway.gif │ ├── h_nthiPathway.gif │ ├── h_nuclearRsPathway.gif │ ├── h_ox40Pathway.gif │ ├── h_p27Pathway.gif │ ├── h_p35AlzheimersPathway.gif │ ├── h_p38mapkPathway.gif │ ├── h_p53Pathway.gif │ ├── h_p53hypoxiaPathway.gif │ ├── h_par1pathway.gif │ ├── h_parkinPathway.gif │ ├── h_parkinsonsPathway.gif │ ├── h_pcafPathway.gif │ ├── h_pdgfPathway.gif │ ├── h_pelp1Pathway.gif │ ├── h_pepiPathway.gif │ ├── h_pgc1aPathway.gif │ ├── h_pitx2Pathway.gif │ ├── h_pkcPathway.gif │ ├── h_plateletAppPathway.gif │ ├── h_plcPathway.gif │ ├── h_plcdPathway.gif │ ├── h_plcePathway.gif │ ├── h_plk3Pathway.gif │ ├── h_pmlPathway.gif │ ├── h_pparPathway.gif │ ├── h_prc2Pathway.gif │ ├── h_prionPathway.gif │ ├── h_ps1Pathway.gif │ ├── h_ptc1Pathway.gif │ ├── h_ptdinsPathway.gif │ ├── h_ptenPathway.gif │ ├── h_pyk2Pathway.gif │ ├── h_rabPathway.gif │ ├── h_rac1Pathway.gif │ ├── h_raccPathway.gif │ ├── h_raccycdPathway.gif │ ├── h_ranMSPathway.gif │ ├── h_ranPathway.gif │ ├── h_ranbp2Pathway.gif │ ├── h_ranklPathway.gif │ ├── h_rarPathway.gif │ ├── h_rarrxrPathway.gif │ ├── h_rasPathway.gif │ ├── h_rbPathway.gif │ ├── h_reckPathway.gif │ ├── h_reelinPathway.gif │ ├── h_relaPathway.gif │ ├── h_rhoPathway.gif │ ├── h_rhodopsinPathway.gif │ ├── h_rnaPathway.gif │ ├── h_s1pPathway.gif │ ├── h_salmonellaPathway.gif │ ├── h_sam68Pathway.gif │ ├── h_setPathway.gif │ ├── h_shhPathway.gif │ ├── h_skp2e2fPathway.gif │ ├── h_slrp2Pathway.gif │ ├── h_slrpPathway.gif │ ├── h_smPathway.gif │ ├── h_soddPathway.gif │ ├── h_sppaPathway.gif │ ├── h_spryPathway.gif │ ├── h_srcRPTPPathway.gif │ ├── h_stat3Pathway.gif │ ├── h_stathminPathway.gif │ ├── h_stemPathway.gif │ ├── h_stressPathway.gif │ ├── h_sumoPathway.gif │ ├── h_tall1Pathway.gif │ ├── h_tcapoptosisPathway.gif │ ├── h_tcrPathway.gif │ ├── h_tcraPathway.gif │ ├── h_tcrmolecule.gif │ ├── h_tcytotoxicPathway.gif │ ├── h_telPathway.gif │ ├── h_tercPathway.gif │ ├── h_tertPathway.gif │ ├── h_tffPathway.gif │ ├── h_tgfbPathway.gif │ ├── h_th1th2Pathway.gif │ ├── h_thelperPathway.gif │ ├── h_tidPathway.gif │ ├── h_tnfr1Pathway.gif │ ├── h_tnfr2Pathway.gif │ ├── h_tob1Pathway.gif │ ├── h_tollPathway.gif │ ├── h_tpoPathway.gif │ ├── h_trkaPathway.gif │ ├── h_tsp1Pathway.gif │ ├── h_tubbyPathway.gif │ ├── h_uCalpainPathway.gif │ ├── h_vdrPathway.gif │ ├── h_vegfPathway.gif │ ├── h_vifPathway.gif │ ├── h_vipPathway.gif │ ├── h_vitCBPathway.gif │ ├── h_vobesityPathway.gif │ ├── h_wnt-Lrp6Pathway.gif │ └── h_wntPathway.gif ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── readme.html ├── reference │ ├── BioCartaImage-package.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── all_pathways.html │ ├── biocartaGrob-1.png │ ├── biocartaGrob.html │ ├── datasets.html │ ├── genes_in_pathway.html │ ├── get_pathway.html │ ├── get_pathway_image-1.png │ ├── get_pathway_image.html │ ├── index.html │ ├── internal.html │ ├── mark_gene-1.png │ ├── mark_gene-2.png │ ├── mark_gene-3.png │ ├── mark_gene.html │ ├── pathwayGrob-1.png │ ├── pathwayGrob.html │ ├── pos_by_polygon.html │ └── print.biocarta_pathway.html └── sitemap.xml ├── inst └── script │ └── process.R ├── man ├── BioCartaImage-package.Rd ├── all_pathways.Rd ├── biocartaGrob.Rd ├── datasets.Rd ├── genes_in_pathway.Rd ├── get_pathway.Rd ├── get_pathway_image.Rd ├── internal.Rd ├── mark_gene.Rd ├── pos_by_polygon.Rd └── print.biocarta_pathway.Rd ├── readme.md ├── tests ├── test-all.R └── testthat │ └── test-general.R └── vignettes └── BioCartaImage.Rmd /.Rbuildignore: 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