Man pages for WubingZhang/rMAUPS
Model-Based Analysis of Ubiquitin-Proteome System Based Protein Degradation.
| arrangePngs | Merge all the rMAUPS results |
| BarView | Bar plot |
| browseProtStructure | View protein sequence positions on protein structure |
| corComplex | Pairwise correlation of proteins within the same protein... |
| Count2TPM | Convert read counts to transcripts per million (TPM) |
| countNA | Quality control of proteomic data |
| CutoffCalling | Quantile of normal distribution. |
| DataCorrelation | Correlation between RNAseq and Protein |
| DEAnalyze | Differential expression analysis |
| DeComplex | Convert gene level differences to pathway level or complex... |
| DensityView | Density plot for gene beta scores in Control and Treatment |
| filterN | Filter out rows with NA or low value |
| getGeneAnn | Retrieve gene annotations from the NCBI, HNSC, and Uniprot... |
| getOrg | Get the kegg code of specific mammalia organism. |
| getOrtAnn | Retreive reference orthologs annotation. |
| gsGetter | Extract pathway annotation from GMT file. |
| gsScore | Calculate score across genes and samples |
| IdentBarView | Identical bar plot |
| imputeNA | Imputation |
| lowAbundanceResampling | low Abundance Resampling method from protein discover |
| MAUPSr | rMAUPS pipeline - QC, differential analysis, integrative... |
| normalizeProteomeDiscoverer | Normalization of ProteomeDiscoverer-exported proteomic data |
| normalizeProteomics | Normalize Fisher's data |
| pcView | Principal component visualization |
| ProteomicsQC | Quality control of proteomic data |
| ReadGMT | ReadGMT |
| readPSPUbiquitin | Reads in the ubiquitination site data from Phosphosite Plus... |
| replicateBasedResampling | Replicate based resampling method from protein discover |
| Residualplot | plot the residuals against the number of quantified... |
| retrieve_gs | Update genesets from source database |
| ScatterView | Scatter plot |
| searchProtSeq | Search protein sequences using a regular expression |
| SpectraCounteBayes | Peptide/Spectra Count Based Empirical Bayes Statistics for... |
| TransformCount | Filter and normalize a count matrix This wrapper function... |
| TransGeneID | Gene ID conversion between ENTREZID and SYMBOL |
| VarianceBoxplot | generate a boxplot of the variance |
| VarianceScatterplot | generate a scatter plot of the variance |
| view | Visulization of rMAUPS results |
| ViolinView | Violin plot |
