Man pages for csoneson/compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
| add_replicates | Add replicates to a tree |
| check_compData | Check the validity of a 'compData' object |
| check_compData_results | Check the validity of a 'compData' result object |
| checkDataObject | Check a list or a 'compData' object for compatibility with... |
| checkParamMatrix | Check Matrix Parameter |
| checkParamVector | Check Vector Parameter |
| check_phyloCompData | Check the validity of a 'phyloCompData' object |
| checkSpecies | Check Species |
| checkTableConsistency | Check consistency of input table to 'runComparison' |
| compcodeR-package | RNAseq data simulation, differential expression analysis and... |
| compData | Create a 'compData' object |
| compData-class | Class compData |
| computeFactorLengths | Compute Length Normalization Factors |
| convertcompDataToList | Convert a 'compData' object to a list |
| convertListTocompData | Convert a list with data and results to a 'compData' object |
| convertListTophyloCompData | Convert a list with data and results to a 'phyloCompData'... |
| convertphyloCompDataToList | Convert a 'phyloCompData' object to a list |
| DESeq2.createRmd | Generate a '.Rmd' file containing code to perform... |
| DESeq2.length.createRmd | Generate a '.Rmd' file containing code to perform... |
| DSS.createRmd | Generate a '.Rmd' file containing code to perform... |
| EBSeq.createRmd | Generate a .Rmd file containing code to perform differential... |
| edgeR.exact.createRmd | Generate a '.Rmd' file containing code to perform... |
| edgeR.GLM.createRmd | Generate a '.Rmd' file containing code to perform... |
| extract_results_phylolm | Extract phylolm results |
| generateCodeHTMLs | Generate HTML file(s) containing code used to run... |
| generateLengths | Simulate a length matrix |
| generateLengthsPhylo | Simulate a length matrix with a phylo model |
| generateSyntheticData | Generate synthetic count data sets |
| get_model_factor | Get the scaling factor |
| getNegativeBinomialDispersion | Get NB dispersion |
| getNegativeBinomialMean | Get NB mean |
| getNegativeBinomialParameters | Get all parameters of the NB at once |
| get_poisson_log_normal_parameters | Compute log means and variances |
| getTree | Get the tree from a phyloCompData object |
| lengthNorm.limma.createRmd | Generate a '.Rmd' file containing code to perform... |
| lengthNorm.sva.limma.createRmd | Generate a '.Rmd' file containing code to perform... |
| listcreateRmd | List available *.createRmd functions |
| logcpm.limma.createRmd | Generate a '.Rmd' file containing code to perform... |
| NBPSeq.createRmd | Generate a '.Rmd' file containing code to perform... |
| NB_to_PLN | Negative Binomial to Poisson Log-Normal |
| nEffNaive | Effective Sample Size |
| nEffRatio | Effective Sample Size Ratio |
| NOISeq.prenorm.createRmd | Generate a '.Rmd' file containing code to perform... |
| phyloCompData | Create a 'phyloCompData' object |
| phyloCompData-class | Class phyloCompData |
| phyloCompDataFromCompData | Create a 'phyloCompData' object |
| phylolm_analysis | Perform the phylolm analysis |
| phylolm.createRmd | Generate a '.Rmd' file containing code to perform... |
| runComparison | Run the performance comparison between differential... |
| runComparisonGUI | A GUI to the main function for running the performance... |
| runComparisonShiny | A shiny-based GUI to the main function for running the... |
| runDiffExp | The main function to run differential expression analysis |
| scale_variance_process | Scale the variances |
| show_compData | Show function for 'compData' object |
| show-compData-method | Show method for 'compData' object |
| show-phyloCompData-method | Show method for 'phyloCompData' object |
| simulateData | Simulate the Data |
| simulateDataPhylo | Simulate the Data using the tree |
| simulatePhyloPoissonLogNormal | Simulate Tree Structured Counts |
| sqrtcpm.limma.createRmd | Generate a '.Rmd' file containing code to perform... |
| summarizeSyntheticDataSet | Summarize a synthetic data set by some diagnostic plots |
| TCC.createRmd | Generate a '.Rmd' file containing code to perform... |
| ttest.createRmd | Generate a '.Rmd' file containing code to perform... |
| voom.limma.createRmd | Generate a '.Rmd' file containing code to perform... |
| voom.ttest.createRmd | Generate a '.Rmd' file containing code to perform... |
| writeNormalization | Generate a '.Rmd' file containing code to normalize data. |
