Man pages for biomics-pasteur-fr/RNADiff
R Tools for RNA-Seq Projects at Institut Pasteur (Biomics Platform)
| averageMatrix | Average a transformed-counts matrix before ploting a heatmap |
| barplotNul | Bar plot of number of null counts per sample |
| barplotTC | Bar plot of total number of counts per sample |
| BCVPlot | BCV plot (for edgeR object) |
| boxplotCounts | Box-plots representing counts distribution per sample |
| checkContrasts | Check the contrasts built manually |
| checkInfoGlength | Check the info and glength files |
| clusterPlot | Dendrogram of sample clustering |
| compareLists | Comparing two lists of features |
| convertUnderscores | Convert underscores for reporting in LaTeX |
| densityPlot | Density plot of all samples |
| diagLogFC | Plot the distribution of the log2 Fold Changes |
| diagLogNormalityDisp | Check the log-normality of the features dispersion estimates |
| diagSizeFactors | Check the right value of sizeFactors |
| down | Extract down-regulated features from a table of results |
| exportComplete.DESeq2 | Export complete data and results from DESeq2 |
| exportComplete.edgeR | Export complete data and results from edgeR |
| geneLengthEffect | Generate some plots to investigate the gene length effect |
| heatmapDE | Heatmap of DE features |
| histoRawp | Histogram of raw p-values |
| loadCountData | Load count files |
| loadTargetFile | Load file containing sample info |
| majSequences | Proportion of reads associated with the three most expressed... |
| MAplotDE | MA-plot of DE features |
| MDSPlot | MDS plot of samples (for edgeR objects) |
| nbDiffSeuil | Number of DE features according to the FDR threshold |
| nDiffTotal | Number of down, up and total per comparison |
| normCounts.edgeR | Normalized counts for edgeR |
| normGeneLength | Remove ribosomal RNA features in all samples |
| pairwiseScatterPlots | Scatter plots for pairwise comparaisons of log counts |
| pairwiseSERE | Pairwise SERE statistics |
| PCAPlot | PCA of samples (for DESeq2 object) |
| plotDispEstimates | Scatter plots representing dispersion estimates vs mean... |
| plotEvolution | Plots of the expression of some interesting features |
| removeNul | Remove features with null counts in all samples |
| RNADiffAnalysis-package | R Tools for RNA-Seq Projects within the Biomics Platform |
| tabIndepFiltering | Table of features discarded by the independent filtering |
| up | Extract up-regulated features from a table of results |
| vennDiagramDE | Venn diagram |
| volcanoPlotDE | volcano-plot of DE features |
