bio-0.4.6: A bioinformatics libraryContentsIndex
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AAProp
Ala
Align
1 (Type/Class)
2 (Data Constructor)
Alignment
aliphatic
Amino
andSameSeq
Ann
Annotation
appendHeader
Arg
aromatic
asksGFF
Asm
Asn
Asp
Assembly
Asx
attrByTag
attributes
attrTag
attrValues
Aux
aux
1 (Function)
2 (Function)
avg
b36
bases
baseToFlowPos
BED
1 (Type/Class)
2 (Data Constructor)
bits
1 (Function)
2 (Function)
blastdate
BlastFlat
1 (Type/Class)
2 (Data Constructor)
BlastHit
1 (Type/Class)
2 (Data Constructor)
BlastMatch
1 (Type/Class)
2 (Data Constructor)
blastn_default
blastprogram
BlastRecord
1 (Type/Class)
2 (Data Constructor)
blastreferences
BlastResult
1 (Type/Class)
2 (Data Constructor)
blastversion
blockcount
blocksizes
blockSizeStart
blosum45
blosum62
blosum80
bounds
1 (Function)
2 (Function)
Branch
castSeq
castToAmino
castToNuc
charged
checkInvariants
1 (Function)
2 (Function)
children
1 (Function)
2 (Function)
childrenM
Chr
chrom
chromEnd
chromosomes
chromStart
clipFlows
clipSeq
clip_adapter_left
clip_adapter_right
clip_qual_left
clip_qual_right
Clustered
cluster_sl
columns
CommonHeader
1 (Type/Class)
2 (Data Constructor)
Comp
compact
compl
complement
contig
ContigLoc
1 (Type/Class)
2 (Data Constructor)
contigLoc
contigous
ContigSeqLoc
convert
countIO
countSeqs
Cys
database
date
dbchars
dbsequences
decCh
decode2Bit
decode36
decodeDate
decodeKO
decodeLocation
decodeReadName
decodeUP
decomment
defragSeq
Del
delete
1 (Function)
2 (Function)
deleteBy
Dir
1 (Type/Class)
2 (Type/Class)
DiscardFilter
display
1 (Function)
2 (Function)
3 (Function)
4 (Function)
displayContigSeqLoc
displaySeqPos
divMods
dlength
E
Edit
EditList
EL
empty
encode2Bit
encode36
encodeDate
encodeLocation
encodeReadName
encodeRegion
end
endPos
1 (Function)
2 (Function)
entropy
Eq
ES
escapeAllBut
escapeAllOf
escapeByteString
ESet
EST
ESTq
EST_long
EST_set
EST_short
eval
EvidenceCode
extend
1 (Function)
2 (Function)
extractGaps
e_val
1 (Function)
2 (Function)
Feature
1 (Type/Class)
2 (Data Constructor)
FeatureHier
FeatureHierSequences
features
1 (Function)
2 (Function)
featureSequence
filter_dots
filter_empty
filter_key
filter_length
filter_mixed
filter_qual20
filter_sigint
flatten
Flow
flow
flowgram
flowgram_fmt
flowToBasePos
flow_data
flow_index
flow_length
fragments
Frame
fromIUPAC
fromList
1 (Function)
2 (Function)
3 (Function)
fromLists
fromN
fromPosLen
fromQ
fromStartEnd
fromStr
ftype
Func
Fwd
1 (Data Constructor)
2 (Data Constructor)
3 (Data Constructor)
gapped
Gaps
geneCDSes
geneCDS_SLM
genes
geneSeqLoc
geneSequence
genkeys
genNonNegOffset
genOffset
genPositiveOffset
genReadKegg
getSequence
GFFAttr
1 (Type/Class)
2 (Data Constructor)
Gln
global_align
1 (Function)
2 (Function)
3 (Function)
global_score
1 (Function)
2 (Function)
3 (Function)
Glu
Glx
Gly
GO
GoClass
GoDef
1 (Type/Class)
2 (Data Constructor)
GoHierarchy
GoTerm
group
hash
hashes
HashF
hasqual
helixP
HF
His
hits
hRead2Bit
hReadFasta
hReadFastQ
hReadPhd
hWrite2Bit
hWriteFasta
hWriteFastaQual
hWriteFastQ
hWriteQual
hydropathy
hydrophobic
h_from
1 (Function)
2 (Function)
h_to
1 (Function)
2 (Function)
IC
IDA
identity
1 (Function)
2 (Function)
ids
IEA
IEP
IGC
IGI
Ile
IMP
Index
index_length
index_offset
indirect
Ins
insert
1 (Function)
2 (Function)
3 (Function)
insertGaps
integralRandomR
IPI
isCurated
isN
isRepl
ISS
isWithin
1 (Function)
2 (Function)
3 (Function)
itemRGB
k2n
k2n'
key
key_length
KO
1 (Type/Class)
2 (Data Constructor)
ksort
KWords
kwords
lazyMany
Leaf
leftoffset
length
1 (Function)
2 (Function)
3 (Function)
4 (Function)
5 (Function)
Leu
lines
Loc
1 (Type/Class)
2 (Data Constructor)
loc
local_align
1 (Function)
2 (Function)
3 (Function)
local_score
1 (Function)
2 (Function)
3 (Function)
LocMap
lookupId
1 (Function)
2 (Function)
lookupIdChildren
lookupOverlaps
1 (Function)
2 (Function)
lookupWithin
1 (Function)
2 (Function)
Lys
mass
match
matches
Met
Minus
Mismatch
1 (Type/Class)
2 (Data Constructor)
mismatch
mismatches
1 (Function)
2 (Function)
mismatchSeqPos
1 (Function)
2 (Function)
mkSeqs
mmoffset
mylines
N
n2i'
n2k
name
1 (Function)
2 (Function)
3 (Function)
4 (Function)
namedSLM
name_length
NAS
ncount
ND
negative
nhit
nmismatch
1 (Function)
2 (Function)
noncodingExons
noncodingSeqLoc
noncodingSequence
NR
Nuc
Nucleotide
num_bases
num_reads
Offset
offset
1 (Function)
2 (Function)
offset5
on
oneOf
onSameSeq
OnSeq
1 (Type/Class)
2 (Data Constructor)
onSeqName
onSeqObj
OnSeqs
or
overlaps
1 (Function)
2 (Function)
3 (Function)
overlap_align
overlap_score
P
packFlows
pairend
pam30
pam70
parentIds
parents
1 (Function)
2 (Function)
parentsM
parse
1 (Function)
2 (Function)
3 (Function)
4 (Function)
5 (Function)
6 (Function)
parseMismatch
parsePSL
parseWithFasta
perSeq
perSeqUpdate
phase
Phe
Plus
polar
Pos
1 (Type/Class)
2 (Data Constructor)
posInto
1 (Function)
2 (Function)
positive
posOutof
1 (Function)
2 (Function)
Pro
Proc
progressive
Protein
PSL
1 (Type/Class)
2 (Data Constructor)
pslHeader
ptest
putSeqLn
Q
qend
qgapcount
qgaplength
qlength
1 (Function)
2 (Function)
qname
qsize
qstart
qstarts
Qual
qual
1 (Function)
2 (Function)
qual20
QualData
Quality
quality
qualMx
qualnt
query
1 (Function)
2 (Function)
queryQual
querySequ
q_from
1 (Function)
2 (Function)
q_to
1 (Function)
2 (Function)
RCA
rcontig
rcpacked
read2Bit
readACE
readbase
readBED
ReadBlock
1 (Type/Class)
2 (Data Constructor)
readFasta
readFastaQual
readFastQ
readGO
readGOA
ReadHeader
1 (Type/Class)
2 (Data Constructor)
ReadName
1 (Type/Class)
2 (Data Constructor)
readnt
readObo
readPhd
readPSL
readQual
reads
readSFF
readTerms
readXML
1 (Function)
2 (Function)
read_header
read_name
recoverSFF
refbase
refCLoc
refCSeqLoc
1 (Function)
2 (Function)
refname
1 (Function)
2 (Function)
refnt
refSeqLoc
1 (Function)
2 (Function)
refSeqPos
1 (Function)
2 (Function)
refstart
region
removePrefix
Repl
repmatch
results
Rev
1 (Data Constructor)
2 (Data Constructor)
RevCompl
revCompl
revcompl
revcompl'
rRNAs
runGFF
runGFFIO
SA
SAM
sameRead
score
1 (Function)
2 (Function)
Selector
Seq
SeqData
seqData
1 (Function)
2 (Function)
3 (Function)
4 (Function)
seqdata
seqDataPadded
1 (Function)
2 (Function)
seqheader
SeqId
seqid
seqlabel
seqlength
SeqLoc
seqLoc
SeqLocMap
seqmap
SeqName
seqNt
seqNtPadded
SeqPos
seqqual
seqToStr
sequ
1 (Function)
2 (Function)
Sequence
sequence'
sequences
Ser
setHeader
SFF
1 (Type/Class)
2 (Data Constructor)
sffToSequence
Shape
showalign
showT
sigint
simpleMx
slength
1 (Function)
2 (Function)
slide
1 (Function)
2 (Function)
small
SoapAlign
SoapAlignMismatch
sortExons
source
splitWhen
start
startPos
1 (Function)
2 (Function)
STP
Strand
1 (Type/Class)
2 (Type/Class)
strand
1 (Function)
2 (Function)
3 (Function)
4 (Function)
5 (Function)
6 (Function)
7 (Function)
Stranded
stranded
strandP
Strands
subject
1 (Function)
2 (Function)
SubstMx
T
TAS
tend
Test
test
1 (Function)
2 (Function)
tgapcount
tgaplength
thickEnd
thickStart
Thr
time
1 (Function)
2 (Function)
tiny
tname
toIUPAC
toStr
toStrings
translate
trim
TrimFilter
trimFromTo
trimKey
Trp
tsize
tstart
tstarts
Tyr
unEscapeByteString
UniProtAcc
Unknown
unpackFlows
unparse
1 (Function)
2 (Function)
3 (Function)
unparseMismatch
unparsePSL
unval
Val
val
withinContigSeqLoc
withNameAndSeq
withSeqData
write2Bit
writeACE
writeBED
writeFasta
writeFastaQual
writeFastQ
writePSL
writeQual
writeSFF
writeSFF'
Xaa
Xle
x_loc
y_loc