Entry: GeneR
Aliases: GeneR
Keywords: utilities
Description: Overview of GeneR package
URL: ../../../library/GeneR/html/01GeneR.html

Entry: globalSeg
Aliases: globalSeg
Keywords: utilities
Description: Class manipulating segments
URL: ../../../library/GeneR/html/02globalSeg.html

Entry: Globals Variables
Aliases: globals
Keywords: utilities
Description: Globals variables on Gene sequences
URL: ../../../library/GeneR/html/02globals.html

Entry: getOrfs
Aliases: getOrfs maxOrf
Keywords: utilities
Description: Gets ORFs from a sequence
URL: ../../../library/GeneR/html/Allorf.html

Entry: AtoR
Aliases: AtoR AtoT RtoA RtoT TtoA TtoR
Keywords: utilities
Description: Conversion of addresses
URL: ../../../library/GeneR/html/AtoR.html

Entry: Match
Aliases: Match
Keywords: utilities
Description: Value Matching
URL: ../../../library/GeneR/html/Match.html

Entry: Xor.globalSeg
Aliases: Xor.globalSeg
Keywords: utilities
Description: Xor for global segments
URL: ../../../library/GeneR/html/Xor.globalSeg.html

Entry: Xor.segSet
Aliases: Xor.segSet xorRecouvr Xor Xor.default
Keywords: utilities
Description: Xor for segments sets
URL: ../../../library/GeneR/html/Xor.segSet.html

Entry: and.globalSeg
Aliases: and.globalSeg &.globalSeg
Keywords: utilities
Description: Intersection of global segments
URL: ../../../library/GeneR/html/and.globalSeg.html

Entry: and.segSet
Aliases: and.segSet and and.default
Keywords: utilities
Description: Intersection of segments
URL: ../../../library/GeneR/html/and.segSet.html

Entry: appendSeq
Aliases: appendSeq
Keywords: utilities
Description: Appends two sequences
URL: ../../../library/GeneR/html/appendSeq.html

Entry: as.globalSeg
Aliases: as.globalSeg as.matrix.globalSeg range.globalSeg
Keywords: utilities
Description: GlobalSeg manipulation
URL: ../../../library/GeneR/html/as.globalSeg.html

Entry: as.segSet
Aliases: as.segSet as.matrix.segSet as.data.frame.segSet plot.segSet
Keywords: utilities
Description: Segments Set manipulation
URL: ../../../library/GeneR/html/as.segSet.html

Entry: assemble
Aliases: assemble
Keywords: utilities
Description: Concatenates parts of a sequence
URL: ../../../library/GeneR/html/assemble.html

Entry: bankDensityProfile
Aliases: bankDensityProfile
Keywords: utilities
Description: Computes density profile(s) of a bank of fasta sequences
URL: ../../../library/GeneR/html/bankDensityProfile.html

Entry: bankSummary
Aliases: bankSummary
Keywords: utilities
Description: Computes informations on all a bank file
URL: ../../../library/GeneR/html/bankSummary.html

Entry: CompoSeq
Aliases: compoSeq strCompoSeq
Keywords: utilities
Description: Composition in mono, di or trinucleotides of a sequence
URL: ../../../library/GeneR/html/compos.seq.html

Entry: Concat
Aliases: concat
Keywords: utilities
Description: Concatenation of two sequences
URL: ../../../library/GeneR/html/concat.html

Entry: deleteCR
Aliases: deleteCR
Keywords: utilities
Description: Delete carriage return in file
URL: ../../../library/GeneR/html/deleteCR.html

Entry: densityProfile
Aliases: densityProfile plot.profile
Keywords: utilities
Description: Density profiles
URL: ../../../library/GeneR/html/densityProfile.html

Entry: DnaToRna
Aliases: dnaToRna rnaToDna
Keywords: utilities
Description: DNA <-> RNA sequence rewriting
URL: ../../../library/GeneR/html/dna.rna.html

Entry: exactWord
Aliases: exactWord
Keywords: utilities
Description: Exact matches of an oligomer
URL: ../../../library/GeneR/html/exact.word.html

Entry: fastaDescription
Aliases: fastaDescription
Keywords: utilities
Description: Description field reading of a fasta sequence
URL: ../../../library/GeneR/html/fasta.descript.html

Entry: Buffers
Aliases: freeSeq freeAllSeq nSeq
Keywords: utilities
Description: Low level functions on buffer manipulation
URL: ../../../library/GeneR/html/free.seq.html

Entry: getAccn
Aliases: getAccn getBegSeq getEndSeq getSeqSize getStrand
Keywords: utilities
Description: Reading of a GeneR global variable
URL: ../../../library/GeneR/html/getAccn.html

Entry: getParam
Aliases: getParam
Keywords: utilities
Description: Reading of all the GeneR global variables
URL: ../../../library/GeneR/html/getParam.html

Entry: getSeq
Aliases: getSeq
Keywords: utilities
Description: Sequence fragments extraction
URL: ../../../library/GeneR/html/getseq.html

Entry: indexFasta
Aliases: indexFasta indexEmbl indexGbk
Keywords: utilities
Description: Index file creation for a sequences bank
URL: ../../../library/GeneR/html/indexfasta.html

Entry: insertSeq
Aliases: insertSeq
Keywords: utilities
Description: Sequence insertion
URL: ../../../library/GeneR/html/insert.html

Entry: lowerSeq
Aliases: lowerSeq upperSeq
Keywords: utilities
Description: Convert upper/lower-case characters in sequence fragments
URL: ../../../library/GeneR/html/lower.html

Entry: makeIndex
Aliases: makeIndex
Keywords: utilities
Description: Index file creation for a bank file (internal function)
URL: ../../../library/GeneR/html/makeIndex.html

Entry: mask
Aliases: mask
Keywords: utilities
Description: Mask regions on a sequence
URL: ../../../library/GeneR/html/mask.html

Entry: not.globalSeg
Aliases: not.globalSeg -.globalSeg
Keywords: utilities
Description: Substraction of globals segments
URL: ../../../library/GeneR/html/not.globalSeg.html

Entry: not.segSet
Aliases: not.segSet -.segSet not not.default
Keywords: utilities
Description: Substraction of segments sets
URL: ../../../library/GeneR/html/not.segSet.html

Entry: or.globalSeg
Aliases: or.globalSeg |.globalSeg
Keywords: utilities
Description: Union of global segments
URL: ../../../library/GeneR/html/or.globalSeg.html

Entry: or.segSet
Aliases: or.segSet unionSeg or or.default
Keywords: utilities
Description: Union of 2 segments sets
URL: ../../../library/GeneR/html/or.segSet.html

Entry: placeString
Aliases: placeString
Keywords: utilities
Description: Sequence loading in a GeneR sequence buffer.
URL: ../../../library/GeneR/html/placestring.html

Entry: plot.globalSeg
Aliases: plot.globalSeg
Keywords: utilities
Description: Plot an object of class globalSeg
URL: ../../../library/GeneR/html/plot.globalSeg.html

Entry: posMaskedSeq
Aliases: posMaskedSeqFile posMaskedSeq
Keywords: utilities
Description: Position of masked fragments
URL: ../../../library/GeneR/html/posMaskedSeq.html

Entry: randomSeq
Aliases: randomSeq shuffleSeq
Keywords: utilities
Description: Create random sequence
URL: ../../../library/GeneR/html/randomSeq.html

Entry: Read location
Aliases: readGbkLocation readEmblLocation
Keywords: utilities database
Description: Get annotations of a GeneBank or an EMBL sequence
URL: ../../../library/GeneR/html/read.gbk.location.html

Entry: readEmblDescript
Aliases: readEmblDescript
Keywords: utilities database
Description: Read features from an Embl bank file
URL: ../../../library/GeneR/html/readEmblDescript.html

Entry: readSeq
Aliases: readSeq readFasta readGbk readEmbl strReadFasta strReadGbk strReadEmbl
Keywords: utilities
Description: Sequence extraction from a bank
URL: ../../../library/GeneR/html/readseq.html

Entry: relist
Aliases: relist relistage
Keywords: utilities
Description: Group segments into global segments
URL: ../../../library/GeneR/html/relist.html

Entry: Reverse complementary
Aliases: revComp strComp
Keywords: utilities
Description: Performs the reverse of a sequence
URL: ../../../library/GeneR/html/revcomp.html

Entry: seqSkew
Aliases: seqSkew GCcontent
Keywords: utilities
Description: compute the strand assymetries from one sequence fragment
URL: ../../../library/GeneR/html/seqSkew.html

Entry: seqSrs
Aliases: seqSrs seqNcbi seqUrl
Keywords: utilities
Description: Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs
URL: ../../../library/GeneR/html/sequrl.html

Entry: SetAccn
Aliases: setAccn setBegSeq setSeqSize setStrand
Keywords: utilities
Description: Set globals variables of a sequence
URL: ../../../library/GeneR/html/setAccn.html

Entry: SetParam
Aliases: setParam
Keywords: utilities
Description: Set global variables associated to a sequence
URL: ../../../library/GeneR/html/setParam.html

Entry: size.globalSeg
Aliases: size size.default size.globalSeg Max.globalSeg Min.globalSeg Length.globalSeg Max Max.default Min Min.default Length Length.default
Keywords: utilities
Description: Size.globalSeg
URL: ../../../library/GeneR/html/size.globalSeg.html

Entry: SizeSeq
Aliases: sizeSeq .seqSize
Keywords: utilities
Description: Size of a sequence in a buffer
URL: ../../../library/GeneR/html/sizeseq.html

Entry: SizeSeqFasta
Aliases: sizeSeqFasta sizeSeqGbk sizeSeqEmbl
Keywords: utilities
Description: Size of a sequence from a fasta/embl/gbk file
URL: ../../../library/GeneR/html/sizeseqfasta.html

Entry: sliceSegment
Aliases: sliceSegment
Keywords: utilities
Description: delineate sub-segments of equal size at both sides of an origin in a segment
URL: ../../../library/GeneR/html/sliceSegment.html

Entry: Translate
Aliases: translate strTranslate showTable
Keywords: utilities
Description: Translation from DNA trinucleotides to proteine
URL: ../../../library/GeneR/html/translation.html

Entry: WriteFasta
Aliases: writeFasta strWriteFasta
Keywords: utilities
Description: Write sequences into fasta file format
URL: ../../../library/GeneR/html/write.fasta.html

Entry: WriteEmblSeq
Aliases: writeEmblLine writeEmbl writeEmblComment writeEmblSeq
Keywords: utilities
Description: Write to Embl file
URL: ../../../library/GeneR/html/writeEMBL.html
