Files in RGLab/MASTdata
This is the data used for the MAST paper
.Rbuildignore
.gitignore
DATADIGEST
DESCRIPTION
NAMESPACE
R/MASTDataPackage.R
R/PRISTDataPackage.R
README.md
data-raw/ProcessAlex.R
data-raw/ProcessMAIT.R
data-raw/datasets.R
data/MASTDataPackage.rda
data/datalist
inst/doc/AdditionalAnalyses.Rmd
inst/doc/AdditionalAnalyses.html
inst/doc/AdditionalAnalysis/AdditionalAnalyses.md
inst/doc/AdditionalAnalysis/figure/mait_cor-1.png
inst/doc/AdditionalAnalysis/figure/mait_pair-1.png
inst/doc/AdditionalAnalysis/figure/mait_parameters-1.png
inst/doc/AdditionalAnalysis/figure/plot_roc-1.png
inst/doc/AdditionalAnalysis/figure/unnamed-chunk-4-1.png
inst/doc/MAITAnalysis/MASTAnalysis.md
inst/doc/MAITAnalysis/figure/any_time_effect-1.png
inst/doc/MAITAnalysis/figure/figure1-1.png
inst/doc/MAITAnalysis/figure/nongeneson-1.png
inst/doc/MAITAnalysis/figure/outlier_stim_DE-1.png
inst/doc/MAITAnalysis/figure/outlier_stim_DE-2.png
inst/doc/MAITAnalysis/figure/residualCor-1.png
inst/doc/MAITAnalysis/figure/residualCor-2.png
inst/doc/MAITAnalysis/figure/residualCor-3.png
inst/doc/MAITAnalysis/figure/residualCor-4.png
inst/doc/MAITAnalysis/figure/residuals-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-1-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-10-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-11-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-12-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-13-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-14-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-14-2.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-16-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-17-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-17-2.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-3-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-5-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-6-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-7-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-10.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-11.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-12.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-2.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-3.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-4.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-5.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-6.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-7.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-8.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-8-9.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-9-1.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-9-2.png
inst/doc/MAITAnalysis/figure/unnamed-chunk-9-3.png
inst/doc/MASTAnalysis.R
inst/doc/MASTAnalysis.Rmd
inst/doc/MASTAnalysis.html
inst/doc/mDCAnalysis.R
inst/doc/mDCAnalysis.Rmd
inst/doc/mDCAnalysis.html
inst/doc/mDCAnalysis/figure/any_time_effect-1.png
inst/doc/mDCAnalysis/figure/figure1-1.png
inst/doc/mDCAnalysis/figure/nongeneson-1.png
inst/doc/mDCAnalysis/figure/outlier_stim_DE-1.png
inst/doc/mDCAnalysis/figure/outlier_stim_DE-2.png
inst/doc/mDCAnalysis/figure/residualCor-1.png
inst/doc/mDCAnalysis/figure/residualCor-2.png
inst/doc/mDCAnalysis/figure/residualCor-3.png
inst/doc/mDCAnalysis/figure/residualCor-4.png
inst/doc/mDCAnalysis/figure/residuals-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-1-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-10-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-11-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-12-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-13-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-14-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-14-2.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-16-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-17-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-17-2.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-3-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-5-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-6-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-7-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-10.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-11.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-12.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-2.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-3.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-4.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-5.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-6.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-7.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-8.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-8-9.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-9-1.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-9-2.png
inst/doc/mDCAnalysis/figure/unnamed-chunk-9-3.png
inst/doc/mDCAnalysis/mDCAnalysis.md
inst/extdata/(2)140702-BRI MAIT ICS-HM.jo
inst/extdata/(2)140702-BRI MAIT ICS-HM.xml
inst/extdata/775998.fcs
inst/extdata/775999.fcs
inst/extdata/776000.fcs
inst/extdata/BTM_for_GSEA_20131008.gmt
inst/extdata/IdToSymbol
inst/extdata/Limma_only.txt
inst/extdata/Logfiles/processing.log
inst/extdata/MAIT_Modules_symbols.rds
inst/extdata/RUVSVAMAIT.pdf
inst/extdata/RUVSVAMAIT.png
inst/extdata/RUVSVAmDC.pdf
inst/extdata/RUVSVAmDC.png
inst/extdata/Shalek_Modules.rds
inst/extdata/Shalek_Modules_symbol.rds
inst/extdata/c2.all.v4.0.symbols.gmt
inst/extdata/c2.cp.kegg.v4.0.symbols.gmt
inst/extdata/c2.cp.reactome.v4.0.symbols.gmt
inst/extdata/c5.all.v4.0.symbols.gmt
inst/extdata/c5.bp.v4.0.symbols.gmt
inst/extdata/c7.all.v4.0.symbols.gmt
inst/extdata/clusters_shalek.rda
inst/extdata/comb_fdr_logfc.rds
inst/extdata/deseq_only.txt
inst/extdata/edger_only.txt
inst/extdata/emory_blood_transcript_modules.rda
inst/extdata/gene_association.mgi
inst/extdata/gsea_result.rds
inst/extdata/gsea_result_mDC.rds
inst/extdata/method_comp_f_qvalue_mDC.rds
inst/extdata/method_comp_logfc_qvalue.rds
inst/extdata/method_comp_logfc_qvalue_mDC.rds
inst/extdata/output/DESeq_Only_GO_Enrichment.html
inst/extdata/output/Figure1.pdf
inst/extdata/output/Figure2.pdf
inst/extdata/output/Figure2.png
inst/extdata/output/Figure3.pdf
inst/extdata/output/Figure3.png
inst/extdata/output/Figure4.pdf
inst/extdata/output/Figure4.png
inst/extdata/output/Figure5.pdf
inst/extdata/output/Figure5.png
inst/extdata/output/Figure6.pdf
inst/extdata/output/Figure6.png
inst/extdata/output/GOenrichmentDifferentMethods.pdf
inst/extdata/output/GSEA_MAIT_limma_ng_only.png
inst/extdata/output/GSEA_in_Non_Responding_Cells.pdf
inst/extdata/output/GSEA_nonresponsive_vs_stim.pdf
inst/extdata/output/GSEA_nonresponsive_vs_stim_gobp.pdf
inst/extdata/output/GSEA_nonresponsive_vs_unstim.pdf
inst/extdata/output/GSEA_nonresponsive_vs_unstim_gobp.pdf
inst/extdata/output/Limma_Only_GO_Enrichment.html
inst/extdata/output/MAIT_GOBP_WithCDR.png
inst/extdata/output/MAIT_GOBP_WithCDR_comparable.png
inst/extdata/output/SCDE_only_GO_enrichment.html
inst/extdata/output/SuppFig_10.pdf
inst/extdata/output/SuppFig_10_a.pdf
inst/extdata/output/Supplement_Figure_LPS_CORE_ANTIVIRAL_RESIDUALS_PCA.pdf
inst/extdata/output/Supplement_Figure_LPS_CORE_ANTIVIRAL_RESIDUALS_PCA.png
inst/extdata/output/Supplementary_Figure_10.pdf
inst/extdata/output/Supplementary_Figure_11.pdf
inst/extdata/output/Supplementary_Figure_11.png
inst/extdata/output/Supplementary_Figure_12.png
inst/extdata/output/Supplementary_Figure_13.pdf
inst/extdata/output/Supplementary_Figure_13.png
inst/extdata/output/Supplementary_Figure_14.pdf
inst/extdata/output/Supplementary_Figure_2.pdf
inst/extdata/output/Supplementary_Figure_4.pdf
inst/extdata/output/Supplementary_Figure_4.png
inst/extdata/output/Supplementary_Figure_6.pdf
inst/extdata/output/Supplementary_Figure_6.png
inst/extdata/output/edgeR_Only_GO_Enrichment.html
inst/extdata/output/gsea_pam_pic.pdf
inst/extdata/rep_list_cd.rds
inst/extdata/rep_list_limma_cd.rds
inst/extdata/rep_list_limma_no.rds
inst/extdata/rep_list_no.rds
inst/extdata/res_gene_hurdle.rds
inst/extdata/res_gene_ng_hurdle.rds
inst/extdata/scde_only.txt
inst/extdata/significant_genes_q001_fc13.rds
inst/extdata/universe.txt
inst/extdata/withCDR.txt
inst/extdata/withoutCDR.txt
inst/extdata/zlm_cond.rds
inst/extdata/zlm_cond_sh.rds
man/MASTDataPackage.Rd
man/sca_alex.Rd
man/sca_mait.Rd
vignettes/.Rhistory
vignettes/.build.timestamp
vignettes/AdditionalAnalyses.Rmd
vignettes/AdditionalAnalyses.html
vignettes/MASTAnalysis.R
vignettes/MASTAnalysis.Rmd
vignettes/MASTAnalysis.html
vignettes/mDCAnalysis.R
vignettes/mDCAnalysis.Rmd
vignettes/mDCAnalysis.html
