A GUI with caching for RNASeq data


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Documentation for package ‘RNASeqGUI’ version 1.1.2

Help Pages

RNASeqGUI-package RNASeqGUI
BaySeqNB Negative Binomial Test
calculateGUI1 Data Exploration Interface
calculateGUI2 Data Analysis Interface
calculateGUI3 Result Inspection Interface
calculateGUI4 Result Comparison Interface
calculateGUI5 Normalization Interface
calculateGUI6 Bam Exploration Interface
calculateGUI7 Read Count Interface
calculate_BaySeq BaySeq Graphical Interface
calculate_DESeq DESeq Graphical Interface
calculate_DESeq2 DESeq2 Graphical Interface
calculate_EdgeR EdgeR Graphical Interface
calculate_NoiSeq NoiSeq Graphical Interface
ChNumber Chromosome Number Histograms
ComponentHist Component Histogram
countDistr Count Distribution Boxplot
countingReads Counting reads per each gene
densityFun Density Function
DESeq DESeq Analysis
EdgeR2 edgeR Analysis
FDRhist FDR Histogram
FDRhistBaySeq FDR Histogram for bayseq results
FQUA Full Quantile Normalization
Heatmap Heatmap
LikelihoodHistBaySeq Likelihood histogram for bayseq results
MeanDiffPlot Mean Difference Plot
meanVariancePlot Mean Variance Plot
NEWDESeq2 DESeq2 Analysis
NoiDE2 NoiSeq differential expression analysis
PCA2fun PCA 3D function
PCAfun PCA function
perBaseQuality Per Base Quality Score
PlotAllCounts Plot All Counts
PlotCounts Plot Counts
PlotFC lot Fold Change from DESeq results
PlotFC2 Plot Fold Change from DESeq2 results
PlotFC3 Plot Fold Change from edgeR results
plotFC_NoiSeq Plot Fold Change from NoiSeq results
plotNtFreq Plot Nucleotide Frequencies
plotQual Plot Quality
probHist Posterior Probability Histogram from NoiSeq results
Pvalues Pvalue Histogram from DESeq results
Pvalues2 Pvalue Histogram from DESeq2 results
QPlotDensity QPlot Density
QPlotHistogram QPplot Histogram
readCount Count reads for each sample
RNASeqGUI RNASeqGUI Main Inteface
RPKM Reads Per Kilobase Per Million Mapped Reads Normalization
summary.BaySeqNB Negative Binomial Test
TMM Trimmed Mean of M-values Normalization
UQUA Upper Quartile Normalization
Venn2de Venn Diagram Two Sets of DE
Venn3de Venn Diagram Three Sets of DE
VolcanoDESeq Volcano plot for DESeq results
VolcanoDESeq2 Volcano plot for DESeq2 results
VolcanoEdgeR Volcano plot for edgeR results
VolcanoNoiSeq Volcano plot for noiseq results