Files in ntyet/rmRNAseq
RNA-Seq Analysis for Repeated-Measures Data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/DESeq2Fit.R
R/TC_CAR1.R
R/all-sim.R
R/data.R
R/edgeRFit.R
R/globals.R
R/multtest.R
R/pauc_out.R
R/shrink.phi.R
R/splineTimeRFit.R
R/teststat.R
R/varbeta.R
R/voomlimmaFit.R
README.Rmd
README.md
cran-comments.md
data/covset.rda
data/dat.rda
data/design.rda
data/res.rda
data/resSymm.rda
man/DESeq2Fit.Rd
man/NewTimeEst.Rd
man/TC_CAR1.Rd
man/TC_CAR1_sc.Rd
man/TimeMin.Rd
man/corr_matrix.Rd
man/covset.Rd
man/dat.Rd
man/design.Rd
man/edgeRFit.Rd
man/estimate.m0.Rd
man/glsCAR1.Rd
man/glsCAR1_loglik.Rd
man/glsSymm.Rd
man/jabes.q.Rd
man/my_splineDiffExprs.Rd
man/myvoom.Rd
man/pauc_out.Rd
man/res.Rd
man/resSymm.Rd
man/sc_CAR1.Rd
man/sc_Symm.Rd
man/shrink.phi.Rd
man/teststat.Rd
man/voomgls_CAR1.Rd
man/voomgls_Symm.Rd
man/voomlimmaFit.Rd
rmRNAseq.Rproj
simulation/.DS_Store
simulation/1-DataCreation.R
simulation/2-DataAnalysis.R
simulation/3-simulation-script.R
simulation/4-allplot.R
simulation/5-additional-simulation.R
simulation/6-additional-simulation-script.R
simulation/DataAnalysis/RFIanalysis-01-08-2019.rds
simulation/DataAnalysis/RFIanalysis.rds
simulation/SimResults/.DS_Store
simulation/SimResults/Scenario_1_Effect_1/.DS_Store
simulation/SimResults/Scenario_1_Effect_1/All_sim_1.rds
simulation/SimResults/Scenario_1_Effect_1/All_sim_2.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_1.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_10.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_11.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_12.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_13.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_14.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_15.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_16.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_17.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_18.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_19.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_2.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_20.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_21.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_22.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_23.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_24.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_25.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_26.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_27.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_28.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_29.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_3.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_30.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_31.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_32.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_33.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_34.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_35.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_36.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_37.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_38.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_39.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_4.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_40.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_41.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_42.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_43.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_44.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_45.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_46.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_47.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_48.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_49.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_5.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_50.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_6.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_7.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_8.rds
simulation/SimResults/Scenario_1_Effect_1/Output_All_sim_9.rds
simulation/SimResults/Scenario_1_Effect_2/.DS_Store
simulation/SimResults/Scenario_1_Effect_2/All_sim_1.rds
simulation/SimResults/Scenario_1_Effect_2/All_sim_2.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_1.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_10.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_11.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_12.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_13.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_14.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_15.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_16.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_17.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_18.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_19.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_2.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_20.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_21.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_22.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_23.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_24.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_25.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_26.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_27.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_28.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_29.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_3.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_30.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_31.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_32.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_33.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_34.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_35.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_36.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_37.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_38.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_39.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_4.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_40.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_41.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_42.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_43.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_44.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_45.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_46.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_47.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_48.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_49.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_5.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_50.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_6.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_7.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_8.rds
simulation/SimResults/Scenario_1_Effect_2/Output_All_sim_9.rds
simulation/SimResults/Scenario_2_Effect_1/.DS_Store
simulation/SimResults/Scenario_2_Effect_1/All_sim_1.rds
simulation/SimResults/Scenario_2_Effect_1/All_sim_2.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_1.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_10.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_11.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_12.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_13.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_14.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_15.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_16.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_17.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_18.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_19.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_2.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_20.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_21.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_22.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_23.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_24.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_25.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_26.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_27.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_28.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_29.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_3.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_30.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_31.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_32.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_33.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_34.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_35.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_36.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_37.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_38.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_39.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_4.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_40.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_41.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_42.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_43.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_44.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_45.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_46.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_47.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_48.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_49.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_5.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_50.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_6.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_7.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_8.rds
simulation/SimResults/Scenario_2_Effect_1/Output_All_sim_9.rds
simulation/SimResults/Scenario_2_Effect_2/.DS_Store
simulation/SimResults/Scenario_2_Effect_2/All_sim_1.rds
simulation/SimResults/Scenario_2_Effect_2/All_sim_2.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_1.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_10.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_11.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_12.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_13.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_14.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_15.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_16.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_17.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_18.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_19.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_2.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_20.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_21.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_22.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_23.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_24.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_25.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_26.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_27.rds
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simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_36.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_37.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_38.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_39.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_4.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_40.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_41.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_42.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_43.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_44.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_45.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_46.rds
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simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_5.rds
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simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_6.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_7.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_8.rds
simulation/SimResults/Scenario_2_Effect_2/Output_All_sim_9.rds
simulation/data-raw/ISS.RNA-seq.count.final.table.txt
simulation/data-raw/ISS.RNA-seq.final.metadata.for.Yet v2.xlsx
simulation/data/rfidata.rds
simulation/figure/.DS_Store
simulation/figure/FDR_SimPlot_Time024.eps
simulation/figure/FDR_SimPlot_Time024.png
simulation/figure/NTP_SimPlot_Time024.eps
simulation/figure/NTP_SimPlot_Time024.png
simulation/figure/PAUC_SimPlot_Time024.eps
simulation/figure/PAUC_SimPlot_Time024.png
simulation/figure/SampleCorreltion_AllGenes.eps
simulation/figure/SampleCorreltion_AllGenes.pdf
simulation/figure/VennDiagramRFI_Time024.eps
simulation/figure/VennDiagramRFI_Time024.pdf
