| aaGapSites-class | Class '"aaGapSites"' |
| addGeneAligns | Reads a bamRange object for a given 'bamReader', 'refGenome'... |
| addGenomeData-ExpressionSet | Add MaxEnt-scores, Exon-Intron junction sequences score to... |
| addGenomeData-gapSites | Add MaxEnt-scores, Exon-Intron junction sequences score to... |
| addHbond | Class '"hbond"': Provides data and functions for calculation... |
| addMaxEnt | addMaxEnt: Extract subset of data contained in given range... |
| alt_X_ranks | alt_left_ranks and alt_right_ranks functions: Identification... |
| annGapSites-class | Class '"annGapSites"' |
| annotate-ExpressionSet | Adds annotation data to existing ExpressionSet (created by... |
| annotation | Annotation functions for 'gapSites' objects |
| as.data.frame-methods | 'as.data.frame' Returning content of data.frame. |
| caRanges-class | Class '"caRanges"' |
| cdRanges-class | Class '"cdRanges"' |
| c-methods | Coercing functions 'c'. |
| countByGeneName | Reads align number for selected gene from multiple BAM-files. |
| cRanges-class | Class '"cRanges"': Centered ranges. |
| dim-methods | 'dim': Return dimensions of contained data.frame. |
| dnaGapSites-class | Class '"dnaGapSites"' |
| dnaRanges | Reads a bamRange object for a given 'bamReader', 'refGenome'... |
| extractByGeneName | extractByGeneName: Extract subset for sites which lie in... |
| extractRange | extractRange: Extract subset from object where records lie in... |
| gapSites | Creating 'gapSites' and 'dnaGapSites' objects. |
| gapSites-class | Class '"gapSites"': Container for tabulated alignment gap... |
| getGapSites | Read 'gapSites' |
| hbond-class | Class '"hbond"' |
| head-methods | 'head' Return first lines of contained data.frame. |
| initialize-methods | 'initialize' Initializing objects. |
| keyProfiler-class | Class '"keyProfiler"' |
| lrCodons | lrCodon methods |
| maxEnt-class | Class '"maxEnt"' |
| merge-methods | 'merge' Merging two objects into one. |
| plotGeneAlignDepth | plotGeneAlignDepth: Plots of read alignment depth for genetic... |
| rangeByGeneName | Reads a bamRange object for a given 'bamReader', 'refGenome'... |
| readCuffGeneFpkm | Reads FPKM values into ExpressionSet. |
| readExpSet | Reads align number or gptm or rpmg value from all given... |
| readMergedBamGaps | Reads an object of type 'gapSites' using a vector of BAM file... |
| readTabledBamGaps | readTabledBamGaps function |
| seqlogo | seqlogo: Plotting sequence logo for 'cdRanges' and... |
| silic_tryp | silic_tryp function |
| sortTable-methods | Sorting contained data with 'sortTable'. |
| SpliceCountSet-class | Class '"SpliceCountSet"' |
| spliceSites-package | Calculate information on splice-sites from gapped alignments... |
| trim | trim and resize methods: trim_left, trim_right, resize_left,... |
| truncate_seq | truncate_seq function |
| truncateSeq | truncateSeq method |
| trypsinCleave | trypsinCleave method |
| uniqueJuncAnn | uniqueJuncAnn method for ExpressionSet |
| write.files | write.files |
| xCodons | xCodon methods |
| xJunc | xJunc methods: lJunc, rJunc, lrJunc |
| xJuncStrand | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
| z[-methods | Methods for Function '['. |
