R for genes and sequences analysis


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Documentation for package `GeneR' version 1.4.2

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allOrfs Get ORFs from a sequence
assemble Create a sequence by gathering parts a sequence
AtoR Conversion of addresses
AtoT Conversion of addresses
compoSeq Composition in mono, di or trinucleotides of a sequence
concat Concatenate two sequences into a third one
dnaToRna Transformation from T to U in a sequence, and the reverse
exactWord Look for motifs in a sequence
fastaDescription Read the description field from a fasta file
freeAllSeq Free all sequences
freeSeq Free one sequence
GeneR Overview of GeneR package
getAccn Return globals variables of a sequence
getBegSeq Return globals variables of a sequence
getEndSeq Return globals variables of a sequence
getParam Give global variables associated to a sequence
getSeq Extract regions from a sequence
getSeqSize Return globals variables of a sequence
getStrand Return globals variables of a sequence
globals Globals variables on Gene sequences
indexEmbl Create an index for a fasta,embl,gbk file
indexFasta Create an index for a fasta,embl,gbk file
indexGbk Create an index for a fasta,embl,gbk file
insertSeq Insert a sequence in another sequence
makeIndex Make an index for a bank file
maxOrf Get ORFs from a sequence
multiExtract Extract regions from a sequence
paramFromIndex Extract parameters from an index file
placeString Put a character string into a sequence buffer.
posMaskedSeq Get all masked regions
readEmbl Read a sequence from a Fasta, Embl or GeneBank file.
readEmblLocation Get features from a GeneBank file
readFasta Read a sequence from a Fasta, Embl or GeneBank file.
readGbk Read a sequence from a Fasta, Embl or GeneBank file.
readGbkLocation Get features from a GeneBank file
readSeq Read a sequence from a Fasta, Embl or GeneBank file.
revComp Performs the reverse of a sequence
rnaToDna Transformation from T to U in a sequence, and the reverse
RtoA Conversion of addresses
RtoT Conversion of addresses
seqNcbi Download a sequence in Fasta / Genbank / Embl format from Ncbi or Srs
seqSize Size of all sequence buffers
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
setEndSeq 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
sizeSeq Size of a sequence in a bufseq
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
str2ascii Convert a string in its ascii code
strComp Performs the reverse of a sequence
strCompoSeq Composition in mono, di or trinucleotides of a sequence
strMultiExtract Extract regions from a sequence
strReadEmbl Read a sequence from a Fasta, Embl or GeneBank file.
strReadFasta Read a sequence from a Fasta, Embl or GeneBank file.
strReadGbk Read a sequence from a Fasta, Embl or GeneBank file.
strTranslate Translation from DNA trinucleotides to proteine
translate Translation from DNA trinucleotides to proteine
TtoA Conversion of addresses
TtoR Conversion of addresses
writeEmblComment Write to Embl file
writeEmblLine Write to Embl file
writeEmblSeq Write to Embl file
writeFasta Write sequences into fasta file format