A B C D E F G I L M N O P R S T U W X misc
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 | Intersection of global segments |
-.globalSeg | Substraction of globals segments |
-.segSet | Substraction of segments sets |
.seqSize | Size of a sequence in a buffer |
|.globalSeg | Union of global segments |