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 |