RNA-Seq Analysis for Repeated-Measures Data

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Documentation for package ‘rmRNAseq’ version 0.1.0

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covset Covariate Set Associated with RFI RNA-seq
dat RFI RNA-seq Data
DESeq2Fit Analysis of LPS RFI RNA-seq data Using DESeq2
design Reparameterized Design Matrix
edgeRFit Analysis of the RFI RNA-seq data Using edgeR
estimate.m0 Estimate Number of True Null Hypotheses Using Histogram-based Method
glsCAR1 Fit General Linear Model with 'corCAR1' Correlation Structure for One Gene
glsCAR1_loglik Calculate REML Log-Likelihood of glsCAR1 model for each gene
glsSymm Fit General Linear Model with 'corSymm' Correlation Structure for One Gene
jabes.q Q-value Using Histogram-based Method
myvoom myvoom function
my_splineDiffExprs Differential expression analysis based on natural cubic spline regression models for time-course data
NewTimeEst Estimate New Time Points
pauc_out Evaluation of Differential Expression Analysis Methods
res Data Containing Results of Our Proposed Method Applying to RFI RNA-seq data
resSymm Data Containing results when analyzing RFI using TC_Symm
sc_CAR1 Simulating Count Data From The Output of Real Data Analysis
sc_Symm Simulating Count Data From The Output of Real Data Analysis (corSymm)
shrink.phi Shrinkaged Estimates of Error Variance
TC_CAR1 RNA-seq Analysis for Repeated-measures Data
TC_CAR1_sc A Wrap Function to analyze a Simulated Data - All Cases
teststat Calculating F-Type Statistics To Test a General Linear Hypothesis
TimeMin Identify Time Points Mapping to 0 and 1
varbeta Recovering a Symmetric Matrix from Its Lower Triangular Matrix
voomgls_CAR1 General Linear Model Using Voom Output
voomgls_Symm General Linear Model Using Voom Output corSymm correlction structure
voomlimmaFit Analysis of RFI RNA-seq data Using voom