Man pages for clsdavid/FBNNet2_public
Fundamental Boolean Model and Networks
| BoolNet_CellCycle_Network | BoolNet CellCycle Network |
| buildProbabilityTreeOnTargetGene | build Probability Tree On the targetGene |
| checkNumeric | A simple function to check a value is numeric or not |
| checkProbabilityTypeData | A simple function to check a value is probability type data. |
| CheckRightTypeTimeseriesData | This function is used to check whether or not the data is the... |
| checkSimilarity | Check the similarity between time series |
| Common_Genes_Clusters | Fundamental Boolean model Example |
| Common_Genes_Leukeamia | Fundamental Boolean model Example |
| constructFBNCube | Create an Orchard cube |
| constructFBNFunctions | An internal function to construct the FBN functions with an... |
| convertInteraction | A function to convert the traditional network interactions to... |
| convertIntoExpressionTree | An internal function to convert a splitted Boolean expression... |
| convertIntoSampleTimeSeries | This method is used to converts normalized timeseries data... |
| convertMinedResultToFBNNetwork | An internal function to convert the mined result to FBN... |
| convertTimeseriesProbsetNameToGeneName | A method that map the row names (probesets) of a specific... |
| convertToBooleanNetworkCollection | A function to convert the traditional Boolean network to... |
| convertToFBNNetwork | Convert a boolean network object to fundamental boolean... |
| ConvertToNetworkGraphicObject | Convert To Network Graphic Object |
| convert_to_NGO | Convert To Dynamic Network Graphic Object |
| DAVID_gene_list | DAVID Gene Annotation data |
| dissolve | A function moves the sub list items to its parent list |
| dividedVectorIntoSmallgroups | An internal function that divides large data into small... |
| doNonParallelWork | Executing a list of processes not in parallel |
| doNonParallelWorkDecrease | Executing a list of processes in parallel with decreasing... |
| doParallelWork | Executing a list of processes in parallel |
| DrawingAttractorInternal | An Internal method to draw attractor internally |
| ExampleNetwork | Example Network data |
| ExampleTimeseriesData | Fundamental Boolean model Example |
| extractGeneStateFromTimeSeriesCube | A function that extract gene states from time series cube |
| FBNBioinformatics | Functions related to Bioinformatics |
| FBNcellcycleNetwork | Fundamental Boolean model Cell Cycle |
| FBNDataReduction | Remove duplicate timeseries sample data |
| FBNExampleNetworks | Example Network data |
| FBNNetwork.Graph | Executing a list of processes in parallel with decreasing... |
| FBNNetwork.Graph.DrawAttractor | A method to draw attractors in the form of dynamic Network |
| filterNetworkConnections | filtering out non regulate genes |
| filterNetworkConnectionsByGenes | Find Backward Network By Genes |
| filterNetworkConnectionsByInputGenes | Find Backward Network By Genes |
| findAllBackwardRelatedGenes | Find Backward Network By Genes |
| findAllForwardRelatedGenes | Find Forward related Network By Genes internal |
| findAllInputGenes | An internal function to find all input genes from a group of... |
| findAllTargetGenes | An internal function to find all target genes from a group of... |
| findBackwardRelatedNetworkByGenes | Find Backward Network By Genes |
| findForwardRelatedNetworkByGenes | Find Forward related Network By Genes |
| flatDeMorganLaw | An internal function to flat a splitted Boolean expression... |
| generateAllCombinationBinary | Generate all combination of binary data based on an vector of... |
| GenerateDynamicNetworkGraphicObject | An Internal method to generate dynamic network graphic... |
| generateFBMNetwork | Generate Fundamental Boolean Model type of Network |
| generateFBNInteraction | generate FBN interaction |
| generateSimilarReport | Generate similarity report |
| generateSimilaryReport | This method compare two timeseries data and generate similar... |
| genereateBoolNetTimeseries | A method to generate BoolNet type of timeseries data for... |
| getFBMSuccessor | This method is used to calculate the next state |
| getGenePrababilities | The main function to main FBN probabilities from time series... |
| getGenePrababilities_advanced | The main function to main FBN probabilities from time series... |
| getGenePrababilities_basic | A function to get gene probabilities |
| getGenePrababilities_measurements | Get the main measurements based on the input data |
| getncbiseq | Retrieving genome sequence data using SeqinR. The code is a... |
| getProbabilityFromFunctionInput | An internal method to get the probability of regulatory... |
| getRelatedGeneTimeseries | A function to reduce the timeseries data based on the gene... |
| getSpecificExpressedGenes | getSpecificExpressedGenes |
| identifyDifferentiallyExpressedGenes | A benchmark type function to test a complete process of FBN... |
| isAppliedDeMorganLaw | An internal function to check a splitted Boolean expression... |
| isAtomNode | An internal function to check if an expression is atomic node |
| isBooleanTypeTimeseriesData | A simple function to check a value is boolean type data. |
| isSatisfied | Is the Gene State Satisfied |
| isSubExpression | An internal function to check if an expression is a sub... |
| Leukeamia_Networks | Fundamental Boolean model Example |
| Leukeamia_Timeseries | Fundamental Boolean model Example |
| loadFBNNetwork | Load FBN network data into a FBN network object |
| mapProbesetNames | This method is used to map probeset names with gene names |
| mapToGeneNameWithhgu133plus2Db | Annotation method |
| mergeClusterNetworks | A function to merge the networks from clustered FBN cube. |
| mergeInteraction | A function to merge the network interactions |
| mergeNetwork | A function to merge tow networks. |
| mineFBNNetwork | Mine FBN Networks from an Orchard cube |
| mineFBNNetworkStage2 | Internal method |
| mineFBNNetworkWithCores | An internal function |
| networkFiltering | A function to filter networks. |
| networkFixUpdate | A method to fix a specific genes in the FBM networks |
| output_annotated_genes | A method to convert a vector of gene names to annotated gene... |
| output_genes | A method to output a vector of gene names separated by comma |
| output_timesereis_based_on_genes | A method to reorder a matrix by a vector |
| plotNetwork | A function to plot the Fundamental boolean networks |
| print.FBMAttractors | A S3 method to print the FBM attractors |
| print.FundamentalBooleanNetwork | A S3 method to print the FBM network |
| process_cube_algorithm | Get the main measurements based on the input data |
| randomGenerateBinary | A method to generate binary data randomly |
| randomSelection | A random selection function denoted as P[] |
| rbind_all_columns | A method to bind two matrix by row |
| reconstructTimeseries | This method is used to reconstruct time series data |
| regenerateInteractions | An internal function to reconstrunct FBN functions |
| removeDuplicates | Internal method |
| removeFistLevelBracket | An internal function to remove the first brasket |
| reorderSampleTimeSeries | This method is used to sort time series order based on... |
| rep_col | A method to duplicate a column |
| rep_row | A method to duplicate a row |
| search_FBN_core | Internal method |
| searchForAttractors | A function to find all possible FBM (Fundamental Boolean... |
| similarityBetweenMatrix | This function is used to compare the similarity of two... |
| splitExpression | A function to split an expression into a vector of input |
| StaticNetwork | Display a static network in a slice |
| StaticNetworkInSlice | Display a dynamic network in a slice |
| transitionStates | A function do the state transition |
| yeastTimeSeries | Yeast Timeseries Data |
