Man pages for NicWir/VisomX
User-Friendly and Comprehensive Analysis and Visualization of Omics Data
| colFmt | Format font color for Markdown reports |
| delete_prefix | Delete Prefix |
| dot-onAttach | Run upon attaching package VisomX |
| fast.write.csv | Write object in CSV file |
| filter_missval | Filter SummarizedExperiment object based on missing values |
| flux_to_map | Create a metabolic map with fluxes and export as SVG file |
| Get.bwss | Compute within group and between group sum of squares... |
| get_prefix | Get the common prefix of words |
| Intersect | Multiple set version of intersect |
| make_se | Create a SummarizedExperiment object from a data frame |
| manual_impute | Imputation by random draws from a manually defined... |
| meanSdPlot | Plot row standard deviations versus row means |
| met.ANOVA.Anal | Perform ANOVA analysis |
| met.FC.Anal | Fold change analysis, unpaired |
| met.FilterVariable | Methods for non-specific filtering of variables |
| met.GetFC | Used by higher functions to calculate fold change |
| met.GetTtestRes | Used by higher functions to retrieve T-test p-values |
| met.impute | Impute missing variables |
| met.initialize | Constructs a dataSet object for storing metabolomics data |
| met.normalize | Data normalization |
| met.PCA.Anal | Perform a Principal Component Analysis |
| met.PerformFeatureFilter | Used by higher functions for non-specific filtering of... |
| met.plot_ANOVA | Visualize p values determined by ANOVA analysis. |
| met.plot_CorrHeatMap_Features | Pattern hunter, plot correlation heatmap |
| met.plot_CorrHeatMap_Samples | Pattern hunter, plot correlation heatmap |
| met.plot_detect | Visualize intensities of compounds with missing values |
| met.plot_FeatureNormSummary | Visualize effect of normalization on feature density... |
| met.plot_heatmap | Create heat map of hierarchically clustered features and... |
| met.plot_ImpVar | Plot PLS important features |
| met.plot_missval | Plot a heatmap of compounds with missing values |
| met.plot_PCA2DLoading | Plot PCA loadings and also set up the matrix for display |
| met.plot_PCA2DScore | Create 2D PCA score plot |
| met.plot_PCA3DLoading | Create 3D PCA loading plot |
| met.plot_PCA3DScore | Create 3D PCA Score plot |
| met.plot_PCAScree | Plot PCA scree plot |
| met.plot_PLS2DLoading | Plot PLS-DA loadings and also set up the matrix for display |
| met.plot_PLS2DScore | Create 2D PLS-DA score plot |
| met.plot_PLS3DLoading | Create 3D PLS-DA loading plot |
| met.plot_PLS3DScore | Create 3D PLS-DA Score plot |
| met.plot_PLS.Crossvalidation | Plot PLS-DA classification performance using different... |
| met.plot_PLS_Imp | Plot PLS important features |
| met.plot_PLSImpScatter | Plot PLS important features |
| met.plot_PLS.Permutation | Plot PLS-DA classification performance using different... |
| met.plot_SampleNormSummary | Visualize effect of normalization on sample density... |
| met.plot_volcano | Volcano Plot |
| met.PLSDA.CV | PLS-DA classification and feature selection |
| met.PLSDA.Permut | Perform PLS-DA permutation |
| met.PLSR.Anal | Partial least squares (PLS) analysis using _oscorespls_... |
| met.PreparePrenormData | Prepare data for normalization |
| met.print_PCA3DLoading | Plot a generated 3D PCA loading plot in RStudio |
| met.print_PCA3DScore | Plot a generated 3D PCA scores plot in RStudio |
| met.print_PLS3DLoading | Plot a generated 3D PLS-DA loading plot in RStudio |
| met.print_PLS3DScore | Plot a generated 3D PLS-DA scores plot in RStudio |
| met.read_data | Construct mSet data container, read metabolomics data, filter... |
| met.report | Generate a markdown report for metabolomics data analysis |
| met.report_test_normalization | Generate a markdown report for the screening of metabolomics... |
| met.SanityCheck | Perform sanity check on metabolomics data |
| met.test_normalization | Test for optimal data processing conditions |
| met.Ttests.Anal | Perform T-test analysis |
| met.UpdateData | Remove defined samples and features from the metabolomics... |
| met.workflow | Perform metabolomics data analysis workflow |
| pathway_enrich | Pathway Enrichment Analysis |
| Perform.permutation | Permutation |
| plot_coverage | Plot coverage of a SummarizedExperiment |
| png_to_gif | Convert PNGs to an animated GIF |
| prot.add_rejections | Add rejections to a SummarizedExperiment |
| prot.boxplot_intensity | Boxplot Intensity |
| prot.filter_missing | Filter proteins based on missing values |
| prot.get_kegg_pathways | Multiple set version of union |
| prot.get_results | Get Results |
| prot.impute | Impute missing values in a SummarizedExperiment object |
| prot.make_unique | Make Unique Proteins |
| prot.normalize_vsn | Normalize the data via variance stabilization normalization |
| prot.pca | PCA Analysis |
| prot.plot_bar | Plot bar plots for protein abundance or fold change |
| prot.plot_corrheatmap | Plot a correlation heatmap |
| prot.plot_density | Generates density plots for a SummarizedExperiment object |
| prot.plot_detect | Plot detectability for a SummarizedExperiment |
| prot.plot_enrichment | Plot pathway enrichment |
| prot.plot_heatmap | Plots a heatmap of the differentially expressed proteins |
| prot.plot_heatmap_all | Plots a heatmap of all protein abundances |
| prot.plot_imputation | Plot imputation results |
| prot.plot_loadings | Plot the loadings of a principal components analysis |
| prot.plot_missval | Plot missing values in SummarizedExperiment |
| prot.plot_numbers | Plot the number of proteins identified in a... |
| prot.plot_pca | Plot Results of Principal Component Analysis |
| prot.plot_screeplot | SCREE plot |
| prot.plot_upset | Plot an UpSet enrichment plot |
| prot.plot_volcano | Plots a volcano plot for a given contrast |
| prot.read_data | Read proteomics data in table format and create... |
| prot.report | Report Proteomics Data |
| prot.test_diff | Test Differential Expression |
| prot_to_map | Title |
| prot.workflow | Run a complete proteomics analysis workflow. |
| read_file | Call the appropriate function required to read a table file... |
| read_flux | Reads flux data from a file or data frame |
| rna.filter_missing | Filter genes based on missing values |
| rna.impute | Impute missing values in a SummarizedExperiment object |
| rna.make_se | Create a SummarizedExperiment object |
| rna.plot_bar | Plot bar plots for gene abundance or fold change |
| rna.plot_corrheatmap | Plot a correlation heatmap |
| rna.plot_heatmap | Plots a heatmap of the differentially expressed genes |
| rna.plot_imputation | Plot imputation results |
| rna.plot_numbers | Plot the number of genes identified in a DESeqDataSet object |
| rna.plot_pca | Plot Results of Principal Component Analysis |
| rna.plot_volcano | Plots a volcano plot for a given contrast |
| rna.read_data | Read Transcriptomics Data |
| rna.report | Generate a transcriptomics analysis report |
| rna.workflow | RNA sequencing workflow |
| Setdiff | Remove the union of the y's from the common x's. |
| svg_to_pdf | Convert SVG to PDF |
| svg_to_png | Convert SVG to PNG (requires Python and InkScape installed) |
| theme_DEP1 | theme_DEP1 |
| theme_DEP2 | Theme DEP2 |
| Union | Multiple set version of union |
