Contents
Index
Biobase-0.1.0.1: Base library for bioinformatics
Index
.*.
Biobase.Types.Ring
.+.
Biobase.Types.Ring
.^.
Biobase.Types.Ring
.^^.
Biobase.Types.Ring
acgu
Biobase.RNA
acguPairs
Biobase.RNA
acguStr
Biobase.RNA
adjustTemperature
Biobase.Vienna.Modification.Temperature
B
Biobase.Infernal.CM
Basepair
Biobase.Turner
BEGL
Biobase.Infernal.CM
BEGR
Biobase.Infernal.CM
BIF
Biobase.Infernal.CM
Branch
Biobase.Infernal.CM
bulgeL
Biobase.Turner.Tables
cgnsP
Biobase.RNA
cguaP
Biobase.RNA
char2nuc
Biobase.RNA
charNucList
Biobase.RNA
charToNucleotide
Biobase.RNA
CM
1 (Type/Class)
Biobase.Infernal.CM
2 (Data Constructor)
Biobase.Infernal.CM
cmMakeLocal
Biobase.Infernal.CM
cmMakeLocalBegin
Biobase.Infernal.CM
cmMakeLocalEnd
Biobase.Infernal.CM
cmNormalizeProbabilities
Biobase.Infernal.CM
CMProb
Biobase.Infernal.CM
cmProb2Score
Biobase.Infernal.CM
CMScore
Biobase.Infernal.CM
cmScore2Prob
Biobase.Infernal.CM
CMType
Biobase.Infernal.CM
cmType
Biobase.Infernal.CM
colAnnotations
Biobase.Infernal.Stockholm
comments
Biobase.Structure
Complex
1 (Type/Class)
Biobase.Structure
2 (Data Constructor)
Biobase.Structure
constR
Biobase.Types.Convert
Convert
Biobase.Types.Convert
convert
Biobase.Types.Convert
D
Biobase.Infernal.CM
dangle3
Biobase.Turner.Tables
dangle5
Biobase.Turner.Tables
dmap
Biobase.Turner.Tables
dotbracket
Biobase.Structure.DotBracket
dotbracketToPairlist
Biobase.Structure.DotBracket
dZipWith
Biobase.Turner.Tables
E
Biobase.Infernal.CM
eacgu
Biobase.RNA
eInf
Biobase.Constants
eMax
Biobase.Constants
Emission
Biobase.Infernal.CM
EmitP
Biobase.Infernal.CM
EmitS
Biobase.Infernal.CM
emptyIV
Biobase.Vienna
emptyTables
Biobase.Vienna
emptyV
Biobase.Vienna
END
Biobase.Infernal.CM
Energy
1 (Type/Class)
Biobase.Types.Energy
2 (Data Constructor)
Biobase.Types.Energy
eNuc
Biobase.Infernal.CM
eNucL
Biobase.Infernal.CM
eNucR
Biobase.Infernal.CM
escore
Biobase.Infernal.CM
exAnnotations
Biobase.Infernal.Stockholm
expm1
Biobase.Types.Partition
export
1 (Function)
Biobase.Vienna.Export.ViennaC
2 (Function)
Biobase.Vienna.Export.ViennaPar
extMM
Biobase.Turner.Tables
fInf
Biobase.Constants
fromFile
1 (Function)
Biobase.Infernal.Stockholm.Import
2 (Function)
Biobase.Infernal.CM.Import
fromString
Biobase.Infernal.CM.Import
fromTurner
Biobase.Vienna.Import.Turner
gasconst
Biobase.Constants
hairpinL
Biobase.Turner.Tables
hairpinLookup
Biobase.Turner.Tables
hairpinMM
Biobase.Turner.Tables
header
Biobase.Infernal.CM
IL
Biobase.Infernal.CM
iloop1x1
Biobase.Turner.Tables
iloop1x2
Biobase.Turner.Tables
iloop1xnMM
Biobase.Turner.Tables
iloop2x2
Biobase.Turner.Tables
iloop2x3MM
Biobase.Turner.Tables
iloopL
Biobase.Turner.Tables
iloopMM
Biobase.Turner.Tables
importPar
Biobase.Vienna.Import.ViennaPar
intermolecularInit
Biobase.Turner.Tables
IR
Biobase.Infernal.CM
isZero
Biobase.Types.Ring
Kelvin
1 (Type/Class)
Biobase.Types.Convert
2 (Data Constructor)
Biobase.Types.Convert
kelvinC0
Biobase.Constants
largeLoop
Biobase.Turner.Tables
len
Biobase.Structure
localBegin
Biobase.Infernal.CM
localBeginPossible
Biobase.Infernal.CM
localBeginProb2Score
Biobase.Infernal.CM
localBeginScore2Prob
Biobase.Infernal.CM
localEnd
Biobase.Infernal.CM
localEndPossible
Biobase.Infernal.CM
localEndProb2Score
Biobase.Infernal.CM
localEndScore2Prob
Biobase.Infernal.CM
log1p
Biobase.Types.Partition
logSum
Biobase.Types.Partition
MATL
Biobase.Infernal.CM
MATP
Biobase.Infernal.CM
MATR
Biobase.Infernal.CM
maxNinio
Biobase.Turner.Tables
mkDashes
Biobase.Structure.Shapes
mkPair
Biobase.Infernal.Stockholm.Import
mkPartition
Biobase.Types.Partition
MkPrimary
Biobase.RNA
mkPrimary
Biobase.RNA
ML
Biobase.Infernal.CM
MP
Biobase.Infernal.CM
MR
Biobase.Infernal.CM
multiHelix
Biobase.Turner.Tables
multiMM
Biobase.Turner.Tables
multiNuc
Biobase.Turner.Tables
multiOffset
Biobase.Turner.Tables
nchildren
Biobase.Infernal.CM
neg
Biobase.Types.Ring
nid
Biobase.Infernal.CM
ninio
Biobase.Turner.Tables
Node
1 (Type/Class)
Biobase.Infernal.CM
2 (Data Constructor)
Biobase.Infernal.CM
nodeMainState
Biobase.Infernal.CM
nodeMainStateAssocs
Biobase.Infernal.CM
nodes
Biobase.Infernal.CM
nodeToString
Biobase.Infernal.CM.Export
NodeType
Biobase.Infernal.CM
nonStandardMax
Biobase.Vienna.Modification.NonStandard
nparents
Biobase.Infernal.CM
npnsP
Biobase.RNA
nstates
Biobase.Infernal.CM
ntag
Biobase.Infernal.CM
ntype
Biobase.Infernal.CM
nucA
Biobase.RNA
nucC
Biobase.RNA
nucCharList
Biobase.RNA
nucE
Biobase.RNA
nucG
Biobase.RNA
Nucleotide
1 (Type/Class)
Biobase.RNA
2 (Data Constructor)
Biobase.RNA
nucleotideToChar
Biobase.RNA
nucU
Biobase.RNA
nullModel
Biobase.Infernal.CM
one
Biobase.Types.Ring
pairings
Biobase.Structure
pairs
Biobase.RNA
pairTable
Biobase.RNA
parseTurner
Biobase.Turner.Import
Partition
1 (Type/Class)
Biobase.Types.Partition
2 (Data Constructor)
Biobase.Types.Partition
partitionTables
Biobase.Vienna.Modification.Partition
Primary
Biobase.RNA
prob2Score
Biobase.Infernal.CM
Ring
Biobase.Types.Ring
ROOT
Biobase.Infernal.CM
S
Biobase.Infernal.CM
schildren
Biobase.Infernal.CM
Score
1 (Type/Class)
Biobase.Types.Score
2 (Data Constructor)
Biobase.Types.Score
score2Prob
Biobase.Infernal.CM
Secondary
1 (Type/Class)
Biobase.Structure
2 (Data Constructor)
Biobase.Structure
semission
Biobase.Infernal.CM
sequences
Biobase.Infernal.Stockholm
sid
Biobase.Infernal.CM
snode
Biobase.Infernal.CM
sparents
Biobase.Infernal.CM
SSExt
Biobase.Structure
SSTree
1 (Type/Class)
Biobase.Structure
2 (Data Constructor)
Biobase.Structure
stack
Biobase.Turner.Tables
stag
Biobase.Infernal.CM
State
1 (Type/Class)
Biobase.Infernal.CM
2 (Data Constructor)
Biobase.Infernal.CM
stateProb2Score
Biobase.Infernal.CM
states
Biobase.Infernal.CM
stateScore2Prob
Biobase.Infernal.CM
statesProb2Score
Biobase.Infernal.CM
statesScore2Prob
Biobase.Infernal.CM
stateToString
Biobase.Infernal.CM.Export
StateType
Biobase.Infernal.CM
Stockholm
1 (Type/Class)
Biobase.Infernal.Stockholm
2 (Data Constructor)
Biobase.Infernal.Stockholm
stringS
Biobase.Infernal.CM.Export
structures
Biobase.Structure
strVpList
Biobase.RNA
stype
Biobase.Infernal.CM
tchild
Biobase.Infernal.CM
Temperature
1 (Type/Class)
Biobase.Turner
2 (Type/Class)
Biobase.Vienna
termAU
Biobase.Turner.Tables
toPair
Biobase.RNA
toShape
Biobase.Structure.Shapes
toShape1
Biobase.Structure.Shapes
toShape2
Biobase.Structure.Shapes
toShape3
Biobase.Structure.Shapes
toShape4
Biobase.Structure.Shapes
toShape5
Biobase.Structure.Shapes
toSSTree
Biobase.Structure
toString
Biobase.Infernal.CM.Export
Transition
1 (Type/Class)
Biobase.Infernal.CM
2 (Data Constructor)
Biobase.Infernal.CM
transitionTargets
Biobase.Infernal.CM
tscore
Biobase.Infernal.CM
tuple2RevVienna
Biobase.RNA
tuple2Vienna
Biobase.RNA
Turner2004
1 (Type/Class)
Biobase.Turner.Tables
2 (Data Constructor)
Biobase.Turner.Tables
turner2004GH
Biobase.Vienna.Default
TurnerEnthalpy
Biobase.Turner
TurnerEntropy
Biobase.Turner
TurnerSet
Biobase.Turner
TurnerTables
Biobase.Turner
unEnergy
Biobase.Types.Energy
unKelvin
Biobase.Types.Convert
unknown
Biobase.Infernal.Stockholm
unPartition
Biobase.Types.Partition
unPartition'
Biobase.Types.Partition
unPrimary
Biobase.RNA
unScore
Biobase.Types.Score
vienna2RevTuple
Biobase.RNA
vienna2Tuple
Biobase.RNA
ViennaEnergyTables
Biobase.Vienna
ViennaIntTables
Biobase.Vienna
ViennaPair
1 (Type/Class)
Biobase.RNA
2 (Data Constructor)
Biobase.RNA
ViennaPartitionTables
Biobase.Vienna
vpAU
Biobase.RNA
vpCG
Biobase.RNA
vpGC
Biobase.RNA
vpGU
Biobase.RNA
vpNP
Biobase.RNA
vpNS
Biobase.RNA
vpStrList
Biobase.RNA
vpUA
Biobase.RNA
vpUG
Biobase.RNA
zero
Biobase.Types.Ring
zipWithPA
Biobase.Turner.Tables