/usr/lib/R/site-library/EBSeq/INDEX is in r-bioc-ebseq 1.18.0-1.
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The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | DenNHist Density plot to compare the empirical q's and
the simulated q's from the fitted beta
distribution.
EBMultiTest Using EM algorithm to calculate the posterior
probabilities of interested patterns in a
multiple condition study
EBSeq_NingLeng-package
EBSeq: RNA-Seq Differential Expression Analysis
on both gene and isoform level
EBTest Using EM algorithm to calculate the posterior
probabilities of being DE
GeneMat The simulated data for two condition gene DE
analysis
GetDEResults Obtain Differential Expression Analysis Results
in a Two-condition Test
GetMultiFC Calculate the Fold Changes for Multiple
Conditions
GetMultiPP Posterior Probability of Each Transcript
GetNg Ng Vector
GetNormalizedMat Calculate normalized expression matrix
GetPP Generate the Posterior Probability of each
transcript.
GetPPMat Posterior Probability of Transcripts
GetPatterns Generate all possible patterns in a multiple
condition study
IsoList The simulated data for two condition isoform DE
analysis
IsoMultiList The simulated data for multiple condition
isoform DE analysis
Likefun Likelihood Function of the NB-Beta Model
LikefunMulti Likelihood Function of the NB-Beta Model In
Multiple Condition Test
LogN The function to run EM (one round) algorithm
for the NB-beta model.
LogNMulti EM algorithm for the NB-beta model in the
multiple condition test
MedianNorm Median Normalization
MultiGeneMat The simulated data for multiple condition gene
DE analysis
PlotPattern Visualize the patterns
PlotPostVsRawFC Plot Posterior FC vs FC
PolyFitPlot Fit the mean-var relationship using polynomial
regression
PostFC Calculate the posterior fold change for each
transcript across conditions
QQP The Quantile-Quantile Plot to compare the
empirical q's and simulated q's from fitted
beta distribution
QuantileNorm Quantile Normalization
RankNorm Rank Normalization
beta.mom Fit the beta distribution by method of moments
crit_fun Calculate the soft threshold for a target FDR
f0 The Prior Predictive Distribution of being EE
f1 The Prior Predictive Distribution of being DE
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