| addAlpha | Adds an alpha value to colors. |
| addGeneIdsCols2HomologsKaKsTable | Extracts the gene pairs' identifiers from the 'Sequence'... |
| addGeneIdsCols2OrthologsKaKsTable | Uses 'gene.1' as the first member of the orthologous gene... |
| alignAAStringSet | Aligns the set of amino acid sequences based on the chemical... |
| alignCDSSetWithAlignedAAsAsGuide | Uses an amino acid multiple sequence alignment to guide the... |
| alignCDSWithAlignedAASeq | Uses an amino acid multiple sequence alignment to guide the... |
| alignCodingSequencesPipeline | Runs the pipeline to align a set of coding sequences: First... |
| alignedForUnalignedAAPos | Computes the position of the unaligned character at argument... |
| annotationBasedShannonEntropy | Compute Shannon Entropy ('entropy') as a measure of... |
| annotationEvolution | Measures annotations gained, lost, and shared between base... |
| annotationMatrix | Generate a 2x2 contingency table for statistical hypothesis... |
| appendToTestedHypotheses | Function appends a row to the argument data.frame 'df', which... |
| axt | Extracts pairs of genes from a CDS multiple sequence... |
| axtForSelectedDistances | Extracts pairs of genes from a CDS multiple sequence... |
| buildPhylogeneticTree | Uses FastTree[MP] to generate a maximum likelihood tree based... |
| cbindAnnotationDescription | Adds a column to 'enrichment.tbl' holding human readable... |
| classSpecificExpressionProfileDists | Computes the within 'stats' of expression profile distances... |
| closestHomolog | Uses pairwise sequence similarity search results in order to... |
| codeml.tmpl | Template for brew to generate the control file used as input... |
| collectNonConservedAnnotations | For each species identifies those annotations that are non... |
| compositeAnnotations | Generates a list of composite Annotations found for the... |
| computeKsPipeline | Runs the pipeline to compute the Ks values of gene pair 'x'... |
| computeOrthologSpecificAnnotationDiversityPerGroup | Wrapper for function... |
| computeSpeciesSpecificAnnotationDiversityPerGroup | Computes the annotation (function) based Shannon Entropy per... |
| conservedOrthologs | Identifies those pairs of orthologous genes where one member... |
| constructAnnotationVectorSpace | For the argument 'genes' construct a vector space based on... |
| correlationRpkmCopyNo | Generates a data.frame of the Genes' names, copy numbers, and... |
| cosAngleVec | Computes the cosine of the angle between the two... |
| cosDiag | Compute cosinus of the angle between argument vector 'x' and... |
| distNormExprVectrs | Returns the vector resulting from subtracting 'e.v.b' from... |
| distVectorClouds | Measures the distance between two vector clouds (see... |
| domainsForPos | Looks up the conserved protein domains (InterPro) that have... |
| enrichedAnnotations | Tests the NULL Hypothesis for each gene (function) annotation... |
| enrichmentTests | Tests for every function annotation in 'case.anno.tbl' the... |
| euclNorm | Computes the Euclidean norm (length) of vector 'x'. |
| expressionProfileDistStatsPerTissues | Extract different 'stats' per tissue specific expression... |
| expressionProfilesDists | Computes the distance ('base::dist') between the expression... |
| exprVecSpaceEvolutionAfterDupl | Based on an expression vector space infers the evolution of... |
| extractFamilyName | Given a character vector regular expressions are applied to... |
| familyExpanded | Alternative method to detect expanded or compressed families... |
| foregroundNodes | Identifies those tip and inner nodes of the phylogenetic tree... |
| formatNodeLabels | For a default phylogentic tree this formats the local support... |
| geneClassesVectorClouds | Invokes 'GeneFamilies::statVectorCloud' on each subset of... |
| geneGroupsAnnotationBasedShannonEntropy | Computes for each gene group in 'groups.ids' the annotation... |
| geneGroupSubfunctionalization | Invokes 'subfunctionalizationAnnotationBased' for all... |
| genePairInRedis | Checks wether in the current Redis server there is an entry... |
| generateContingencyTable | Generates a matrix that can directly be used as input for... |
| getFamilyDNAStringSet | Extracts the coding sequences of the gene members of the... |
| getMcCores | Reads out SHELL environment variable 'MCCORES' and returns it... |
| getPairsFromDistForIndices | Identifies the pairs that match the argument indices 'k' in... |
| getSpeciesNodeNumberFromCafe | Extracts the number CAFE assigned the species during its... |
| getSpliceVariantSeqs | Identifies those entries in argument 'seq.lst' that have... |
| goEnrichTest | Computes a Gene Ontology (GO) enrichment test using the... |
| hasInvalidVecSpaceComponents | Generic function to check wether any vector component is... |
| hasInvalidVecSpaceComponents.data.frame | Generic function to check wether any vector component is... |
| hasInvalidVecSpaceComponents.matrix | Generic function to check wether any vector component is... |
| hasInvalidVecSpaceComponents.numeric | Generic function to check wether any vector component is... |
| homologs | Identify homologous gene pairs in a table of significantly... |
| hyphy.branch.site.bf | Brew template to generate a family's BranchREL input file |
| hyphy.busted.bf | Brew template to generate a family's BUSTED input file |
| hyphy.fubar.bf | Brew template to generate a family's FUBAR input file |
| hyphy.meme.bf | Brew template to generate a family's MEME input file |
| inferExpectedFalsePositiveRate | Translates the FUBAR reported expected absolute NUMBER of... |
| interVsIntraSpeciesExpressionProfileDists | Extracts the inter- and intra-species distances from argument... |
| iprWithSelectedAA | Identifies conserved protein domains (InterPro) overlapping... |
| joinGOEnrichResults | Method extracts all GO ontology specific enrichment result... |
| KaKsStatistics | Uses KaKs_Calculator for selected pairs of aligned coding... |
| loadDnaFasta | Simple wrapper around seqinr::read.fasta for DNA data.... |
| matchingSpliceVariant | Assuming 'gene.ids' holds gene identifiers that lack splice... |
| maxMinusMin | Computes the absolute distance between maximum and minimum,... |
| maxValuesFromInterVsIntraSpeciesExpressionProfileDists | Generates a data.frame with one row for each family with... |
| mclDataFrameAsList | Converts the data.frame of gene families into a list of gene... |
| mr.bayes.cds.tree | Brew template to generate an Mr Bayes input file for a... |
| mrBayesCdsTree | Generates a valid input file for Mr Bayes, which will... |
| mr.bayes.mixed.cds.tree | Brew template to generate a coding sequences group's Mr Bayes... |
| mr.bayes.mixed.prot.tree | Brew template to generate a protein group's Mr Bayes input... |
| mrBayesProteinTree | Generates a valid input file for Mr Bayes, which will... |
| mrBayesProteinTreeFromMixedMSA | Generates a valid input file for Mr Bayes, which will... |
| mr.bayes.prot.tree | Brew template to generate a protein group's Mr Bayes input... |
| mrBayesTreeFromMixedMSA | Generates a valid input file for Mr Bayes, which will... |
| naAsZero | Helper function that converts argument 'x' to the number zero... |
| nonConservedAnnotations | Identifies those gene annotations that are non conserved... |
| nonConservedCompositeAnnotations | Identifies those composite annotations that are less frequent... |
| normalizeVector | Normalizes the vector 'x' to length 1.0. |
| numberAnnotations | Counts the number of times an annotation, e.g. a Pfam or... |
| orthologs | Identifies orthologous gene pairs as genes being... |
| orthologsFromBLATpslTable | Parses 'psl' default BLAT output formatted files to infer... |
| parseCafeBranchSpecificPValues | Extract the branch specific extension / contraction P-Values... |
| parseMemeBranchResults | Parses a HyPhy MEME branch result file to extract significant... |
| passSupportValues | Passes support values from inner nodes in argument 'trees' to... |
| perpVecToDiagonal | Drops a perpendicular from vector 'x' to the vector space's... |
| plotSpeciesSpecificAnnotationDiversity | Scatter-Plots the pecies specific annotation (function)... |
| plotSpeciesSpecificAnnotationDiversityDists | Boxplots the distributions of species specific annotation... |
| plotTissueSpecificExpressionProfileDistanceDistribs | Plots horizontal boxplots of per tissue distributions of... |
| procGOHyperGResult | Converts an instance of GOHyperGResult into a table... |
| putGenePairIntoRedis | Puts the integer value 1 into the Redis Server using the... |
| rad2deg | Converts an angle's size given in 'radians' to 'degrees'. |
| readBlatPSLoutput | Wraps function base::read.table with the proper arguments... |
| readFubarTable | Parses a FUBAR output table for significant posterior... |
| readInterProScanResultTable | Parses the result file of InterProScan into a data.frame. |
| readKaKsCalculatorOutput | Uses base::read.table to parse the output of... |
| readMclOutput | Uses Linux's AWK and package data.table to parse the output... |
| readMinimumInterProScanResultTable | Uses function... |
| removeDuplicatedInversePairs | Identifies duplicated inverse pairs and discards them. |
| removeExpressionVariant | Modifies the argument 'gene.ids' by deleting expression... |
| removeNodeLabelsAndBranchLengths | Removes node labels and branch lengths from instance of... |
| removeSpliceVariant | Removes trailing splice variant identifier from gene IDs;... |
| renderCodemlInputs | Generates the tree and control file to run PAML's codeml in... |
| replaceSanitizedWithOriginalIDs | Replaces sanitized protein identifiers in XStringSet... |
| replaceWithOriginal | Returns the matching original names for the sanitized ones... |
| replaceWithOriginalInFigTree | Uses GNU sed to replace the sanitized gene identifiers with... |
| sanitizeNames | Many programs in Bioinformatics cannot handle gene accessions... |
| scalarProjection | Computes the scalar projection of vector 'a' onto vector 'b',... |
| selectGeneGroupSpecificEnrichedAnnotations | Infer enriched annotations specific to the argument type of... |
| selectSignificantEnrichments | Filters 'enrichment.tbl' for those annotations that have a... |
| selectSignificantlyEnrichedAnnotations | Selects those results obtained from calling... |
| shannonEntropy | Computes the normalized empirical Shannon Entropy for counts... |
| speciesComposition | Infers the number of genes belonging to the given species. |
| speciesCompositionsToDataFrame | Generate a data frame of the list of species composition... |
| speciesForGeneId | Identifies the species of a gene identifier using the... |
| speciesForGeneId_Regex | Identifies the species of a gene identifier using regular... |
| spec.regex.gene.ids | #################### Define constants: # ####################... |
| statVectorCloud | Computes the statistic 'stat' (default is 'base::mean')... |
| subfunctionalizationAnnotationBased | Identifies instances of subfunctionalization occurred in the... |
| subTrees | Identifies a list of sub-trees in argument tree initiating... |
| testAlignedForUnalignedAAPos | Test for function 'alignedForUnalignedAAPos'. |
| testAnnotationBasedSpeciesSpecificNeofunctionalization | Statistically tests the NULL Hypotheses that the annotation... |
| testExprVecSpaceEvolutionAfterDupl | Testing function 'exprVecSpaceEvolutionAfterDupl'. |
| testGetPairsFromDistForIndices | Tests the function 'getPairsFromDistForIndices'. |
| testHomologs | Test of function 'homologs(...)' |
| testHourglassModel | Test the hypothesis of the developmental hourglass by... |
| testNonConservedAnnotations | Test function 'nonConservedAnnotations' |
| testNonConservedCompositeAnnotations | Test for function nonConservedCompositeAnnotations. |
| testShannonEntropy | Testing function 'GeneFamilies::shannonEntropy' |
| testSubfunctionalizationAnnotationBased | Testing 'subfunctionalizationAnnotationBased' |
| transcriptsPerKilobaseMillion | Calculates Reads Per Kilobase Million (RPKM) RPKM = (Rg *... |
| translate2AASeqs | Uses the program MACSE to translate the coding sequences to... |
| tree4Busted | Annotates a phylogenetic tree in such amanner that foreground... |
| unalignedAAforAlignedAAPos | Computes the position in the unaligned sequence of a... |
| upperWhisker | Identifies the value that corresponds to the upper whisker... |
| validateAASeqs | Validates an AAString |
| validateAAStringSet | Validates an AAStringSet |
| vectorProjection | Computes the vector projection of vector 'a' onto vector 'b',... |
| writeAxt | Writes pairwise aligned sequences to a file of AXT format for... |
