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A B C D E F G I L M N O P R S T U W X misc
| &.globalSeg | Intersection of global segments |
| -.globalSeg | Substraction of globals segments |
| -.segSet | Substraction of segments sets |
| .seqSize | Size of a sequence in a buffer |
| and | Intersection of segments |
| and.default | Intersection of segments |
| and.globalSeg | Intersection of global segments |
| and.segSet | Intersection of segments |
| appendSeq | Appends two sequences |
| as.data.frame.segSet | Segments Set manipulation |
| as.globalSeg | GlobalSeg manipulation |
| as.matrix.globalSeg | GlobalSeg manipulation |
| as.matrix.segSet | Segments Set manipulation |
| as.segSet | Segments Set manipulation |
| assemble | Concatenates parts of a sequence |
| AtoR | Conversion of addresses |
| AtoT | Conversion of addresses |
| bankDensityProfile | Computes density profile(s) of a bank of fasta sequences |
| bankSummary | Computes informations on all a bank file |
| compoSeq | Composition in mono, di or trinucleotides of a sequence |
| concat | Concatenation of two sequences |
| deleteCR | Delete carriage return in file |
| densityProfile | Density profiles |
| dnaToRna | DNA <-> RNA sequence rewriting |
| exactWord | Exact matches of an oligomer |
| fastaDescription | Description field reading of a fasta sequence |
| freeAllSeq | Low level functions on buffer manipulation |
| freeSeq | Low level functions on buffer manipulation |
| GCcontent | compute the strand assymetries from one sequence fragment |
| GeneR | Overview of GeneR package |
| getAccn | Reading of a GeneR global variable |
| getBegSeq | Reading of a GeneR global variable |
| getEndSeq | Reading of a GeneR global variable |
| getOrfs | Gets ORFs from a sequence |
| getParam | Reading of all the GeneR global variables |
| getSeq | Sequence fragments extraction |
| getSeqSize | Reading of a GeneR global variable |
| getStrand | Reading of a GeneR global variable |
| globals | Globals variables on Gene sequences |
| globalSeg | Class manipulating segments |
| indexEmbl | Index file creation for a sequences bank |
| indexFasta | Index file creation for a sequences bank |
| indexGbk | Index file creation for a sequences bank |
| insertSeq | Sequence insertion |
| Length | Size.globalSeg |
| Length.default | Size.globalSeg |
| Length.globalSeg | Size.globalSeg |
| lowerSeq | Convert upper/lower-case characters in sequence fragments |
| makeIndex | Index file creation for a bank file (internal function) |
| mask | Mask regions on a sequence |
| Match | Value Matching |
| Max | Size.globalSeg |
| Max.default | Size.globalSeg |
| Max.globalSeg | Size.globalSeg |
| maxOrf | Gets ORFs from a sequence |
| Min | Size.globalSeg |
| Min.default | Size.globalSeg |
| Min.globalSeg | Size.globalSeg |
| not | Substraction of segments sets |
| not.default | Substraction of segments sets |
| not.globalSeg | Substraction of globals segments |
| not.segSet | Substraction of segments sets |
| nSeq | Low level functions on buffer manipulation |
| or | Union of 2 segments sets |
| or.default | Union of 2 segments sets |
| or.globalSeg | Union of global segments |
| or.segSet | Union of 2 segments sets |
| placeString | Sequence loading in a GeneR sequence buffer. |
| plot.globalSeg | Plot an object of class globalSeg |
| plot.profile | Density profiles |
| plot.segSet | Segments Set manipulation |
| posMaskedSeq | Position of masked fragments |
| posMaskedSeqFile | Position of masked fragments |
| randomSeq | Create random sequence |
| range.globalSeg | GlobalSeg manipulation |
| readEmbl | Sequence extraction from a bank |
| readEmblDescript | Read features from an Embl bank file |
| readEmblLocation | Get annotations of a GeneBank or an EMBL sequence |
| readFasta | Sequence extraction from a bank |
| readGbk | Sequence extraction from a bank |
| readGbkLocation | Get annotations of a GeneBank or an EMBL sequence |
| readSeq | Sequence extraction from a bank |
| relist | Group segments into global segments |
| relistage | Group segments into global segments |
| revComp | Performs the reverse of a sequence |
| rnaToDna | DNA <-> RNA sequence rewriting |
| RtoA | Conversion of addresses |
| RtoT | Conversion of addresses |
| seqNcbi | Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs |
| seqSkew | compute the strand assymetries from one sequence fragment |
| seqSrs | Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs |
| seqUrl | Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs |
| setAccn | Set globals variables of a sequence |
| setBegSeq | Set globals variables of a sequence |
| setParam | Set global variables associated to a sequence |
| setSeqSize | Set globals variables of a sequence |
| setStrand | Set globals variables of a sequence |
| showTable | Translation from DNA trinucleotides to proteine |
| shuffleSeq | Create random sequence |
| size | Size.globalSeg |
| size.default | Size.globalSeg |
| size.globalSeg | Size.globalSeg |
| sizeSeq | Size of a sequence in a buffer |
| sizeSeqEmbl | Size of a sequence from a fasta/embl/gbk file |
| sizeSeqFasta | Size of a sequence from a fasta/embl/gbk file |
| sizeSeqGbk | Size of a sequence from a fasta/embl/gbk file |
| sliceSegment | delineate sub-segments of equal size at both sides of an origin in a segment |
| strComp | Performs the reverse of a sequence |
| strCompoSeq | Composition in mono, di or trinucleotides of a sequence |
| strReadEmbl | Sequence extraction from a bank |
| strReadFasta | Sequence extraction from a bank |
| strReadGbk | Sequence extraction from a bank |
| strTranslate | Translation from DNA trinucleotides to proteine |
| strWriteFasta | Write sequences into fasta file format |
| translate | Translation from DNA trinucleotides to proteine |
| TtoA | Conversion of addresses |
| TtoR | Conversion of addresses |
| unionSeg | Union of 2 segments sets |
| upperSeq | Convert upper/lower-case characters in sequence fragments |
| writeEmbl | Write to Embl file |
| writeEmblComment | Write to Embl file |
| writeEmblLine | Write to Embl file |
| writeEmblSeq | Write to Embl file |
| writeFasta | Write sequences into fasta file format |
| Xor | Xor for segments sets |
| Xor.default | Xor for segments sets |
| Xor.globalSeg | Xor for global segments |
| Xor.segSet | Xor for segments sets |
| xorRecouvr | Xor for segments sets |
| |.globalSeg | Union of global segments |