Documentation for bioroebe (0.10.80)

Alphabetic Index

File Listing

README

Namespace Listing A-Z

Top Level Namespace

A

AdvancedDotplot (Bioroebe)
AlignOpenReadingFrames (Bioroebe)
Alignment (Bioroebe::GUI::LibUI)
Alignment (Bioroebe)
Alignment (Bioroebe::GUI::Gtk)
AlphaHelix (Bioroebe)
AminoacidComposition (Bioroebe::GUI::Tk)
AminoacidComposition (Bioroebe::GUI::Gtk)
AminoacidSubstitution (Bioroebe)
AminoacidsMassTable (Bioroebe)
AnalyseGlycosylationPattern (Bioroebe)
AnalyseLocalDataset (Bioroebe)
AntiSenseStrand (Bioroebe::GUI::Gtk)
AntiSenseStrand (Bioroebe::GUI)
ArgumentError (Bioroebe::Biomart)
Attribute (Bioroebe::Biomart)
AttributeError (Bioroebe::Biomart)
AutocorrectTheNameOfThisFastaFile (Bioroebe)

B

Base (Bioroebe)
BiolangParser (Bioroebe)
Biomart (Bioroebe)
BiomartError (Bioroebe::Biomart)
Bioroebe
Blosum (Bioroebe)
BlosumMatrixViewer (Bioroebe::GUI::Gtk)
BlosumMatrixViewer (Bioroebe::GUI::LibUI)
BlosumMatrixViewer (Bioroebe::GUI::Jruby)
BlosumMatrixViewer (Bioroebe::GUI::Tk)
BlosumMatrixViewerModule (Bioroebe::GUI)
BlosumParser (Bioroebe)
Buried (Bioroebe::ColourScheme)

C

CalculateBlosumScore (Bioroebe)
CalculateCellNumbersOfBacteria (Bioroebe::GUI::LibUI)
CalculateCellNumbersOfBacteria (Bioroebe::GUI::Gtk)
CalculateCellNumbersOfBacteriaModule (Bioroebe::GUI)
CalculateGCContent (Bioroebe)
CalculateMeltingTemperature (Bioroebe)
CalculateMeltingTemperatureForMoreThanThirteenNucleotides (Bioroebe)
CalculateThePositionSpecificScoringMatrix (Bioroebe)
Cell (Bioroebe)
Chart (Bioroebe::Taxonomy)
CheckAvailable (Bioroebe::Taxonomy)
CheckForMismatches (Bioroebe)
CodonPercentage (Bioroebe)
CodonTable (Bioroebe)
CodonTables (Bioroebe)
CodonTablesFrequencies (Bioroebe)
ColourScheme (Bioroebe)
ColourSchemeDemo (Bioroebe)
ColourizeHydrophilicAndHydrophobicAminoacids (Bioroebe)
ColourizeSequence (Bioroebe)
ColoursForBase (Bioroebe)
CommandlineApplication (Bioroebe)
CommandlineArguments (Bioroebe)
CompactFastaFile (Bioroebe)
Compacter (Bioroebe)
ComplementaryDnaStrand (Bioroebe)
Compseq (Bioroebe)
Configuration (Bioroebe)
Consensus (Bioroebe::ColourScheme)
ConsensusSequence (Bioroebe)
Constants (Bioroebe::Taxonomy)
Controller (Bioroebe::GUI::Gtk)
ConvertAminoacidToDNA (Bioroebe)
CoordinateAnalyzer (Bioroebe::ElectronMicroscopy)
CountAmountOfAminoacids (Bioroebe)
CountAmountOfNucleotides (Bioroebe)
CreateAnnotationFormat (Bioroebe)
CreateBatchEntrezFile (Bioroebe)
CreateRandomAminoacids (Bioroebe)
CustomizedDialog (Bioroebe::GUI::Gtk)

D

DNA (Bioroebe)
Database (Bioroebe::Biomart)
Dataset (Bioroebe::Biomart)
DatasetError (Bioroebe::Biomart)
DeduceAminoacidSequence (Bioroebe)
DetectMinimalCodon (Bioroebe)
DetermineAntigenicAreas (Bioroebe)
DetermineMissingNucleotidesPercentage (Bioroebe)
DetermineOptimalCodons (Bioroebe)
Digestion (Bioroebe)
DisplayAminoacidTable (Bioroebe)
DisplayHowManyFastaEntriesAreInThisDirectory (Bioroebe)
DisplayOpenReadingFrames (Bioroebe)
DnaToAminoacidSequence (Bioroebe)
DnaToAminoacidWidget (Bioroebe::GUI::LibUI)
DnaToAminoacidWidget (Bioroebe::GUI::Gtk)
DnaToReverseComplementWidget (Bioroebe::GUI::Gtk)
DnaToReverseComplementWidget (Bioroebe::GUI::LibUI)
DnaToReverseComplementWidgetModule (Bioroebe::GUI)
DotAlignment (Bioroebe)
Dotplot (Bioroebe)
DownloadFasta (Bioroebe)
DownloadFilesFromRebase (Bioroebe)
DownloadTaxonomyDatabase (Bioroebe)

E

ElectronMicroscopy (Bioroebe)
EmbeddableInterface (Bioroebe)

F

FastaDefline (Bioroebe)
FastaParser (Bioroebe)
FastaTableWidget (Bioroebe::GUI::Gtk)
FastqFormatExplainer (Bioroebe)
FetchFastaSequenceFromPdb (Bioroebe)
Filter (Bioroebe::Biomart)
FilterError (Bioroebe::Biomart)
FindGene (Bioroebe)
FindLongestSubstring (Bioroebe)
FindLongestSubstringViaLCSalgorithm (Bioroebe)
FixPosFile (Bioroebe::ElectronMicroscopy)
FormatConverter (Bioroebe::GUI::Gtk)

G

GFF (Bioroebe::Parser)
GUI (Bioroebe)
GenbankFlatFileFormatGenerator (Bioroebe)
GenbankParser (Bioroebe)
Gene (Bioroebe::GUI::Gtk)
Gene (Bioroebe)
GenerateEm2emFile (Bioroebe::ElectronMicroscopy)
GenomePattern (Bioroebe)
GenomeRetriever (Bioroebe)
Glyph (Bioroebe::SVG)
Gtk (Bioroebe::GUI)

H

HTTPError (Bioroebe::Biomart)
HammingDistance (Bioroebe::GUI::LibUI)
HammingDistance (Bioroebe::GUI::Gtk)
HammingDistance (Bioroebe::GUI::Tk)
HammingDistance (Bioroebe)
Helix (Bioroebe::ColourScheme)
HelixWheel (Bioroebe)
Help (Bioroebe::Shell)
Helpline (Bioroebe::Taxonomy)
Hydropathy (Bioroebe::ColourScheme)

I

Info (Bioroebe::Taxonomy)
Interactive (Bioroebe::Taxonomy)
InvalidAminoacid (Bioroebe)
IsDNA (Bioroebe::Taxonomy)

J

Jruby (Bioroebe::GUI)

L

LengthModifier (Bioroebe)
Levensthein (Bioroebe)
LevenstheinDistance (Bioroebe::GUI::Gtk)
LevenstheinDistance (Bioroebe::GUI::Tk)
LevenstheinDistance (Bioroebe::GUI::LibUI)
LevenstheinDistanceModule (Bioroebe::GUI)
LibUI (Bioroebe::GUI)

M

MatplotlibGenerator (Bioroebe)
Matrix (Bioroebe)
MiniFeature (Bioroebe::SVG)
MirrorRepeat (Bioroebe)
MolecularWeightOfNucleotides (Bioroebe)
MostLikelyNucleotideSequenceForThisAminoacidSequence (Bioroebe)
MoveFileToItsCorrectLocation (Bioroebe)

N

Ncbi (Bioroebe)
Node (Bioroebe::Taxonomy)
Nucleotide (Bioroebe::ColourScheme::Helix)
NucleotideAnalyser (Bioroebe::GUI::Gtk)
NucleotideModule (Bioroebe)

P

Page (Bioroebe::SVG)
Palindrome2DStructure (Bioroebe)
PalindromeFinder (Bioroebe)
PalindromeGenerator (Bioroebe)
ParseCoordinates (Bioroebe::ElectronMicroscopy)
ParseEMBL (Bioroebe)
ParseFasta (Bioroebe)
ParseFasta (Bioroebe::Taxonomy)
ParseFastq (Bioroebe)
ParseFrequencyTable (Bioroebe)
ParsePdbFile (Bioroebe)
ParsePdbFile (Bioroebe::GUI::Gtk)
ParseTaxonomy (Bioroebe)
ParsemmCIFFile (Bioroebe)
Parser (Bioroebe)
Pathways (Bioroebe)
Permutations (Bioroebe)
PhredQualityScoreTable (Bioroebe)
PossibleCodonsForThisAminoacid (Bioroebe)
Postgresql (Bioroebe)
PrimerDesignWidget (Bioroebe::GUI::Gtk)
Primitive (Bioroebe::SVG)
ProfilePattern (Bioroebe)
Protein (Bioroebe)
ProteinToDNA (Bioroebe::GUI::LibUI)
ProteinToDNA (Bioroebe::GUI::Gtk)
ProteinToDNAModule (Bioroebe::GUI)
Punnet (Bioroebe)

Q

Quiz (Bioroebe)

R

RGG_Scanner (Bioroebe)
RNALfoldWrapper (Bioroebe)
RandomSequence (Bioroebe::GUI::Gtk)
RandomSequence (Bioroebe::GUI::LibUI)
RawSequence (Bioroebe)
ReadFileXMD (Bioroebe::ElectronMicroscopy)
ReportSecondaryStructuresFromThisPdbFile (Bioroebe)
RestrictionEnzyme (Bioroebe)
RestrictionEnzymes (Bioroebe::GUI::Gtk)
ReverseComplement (Bioroebe)
Ruler (Bioroebe)

S

SVG (Bioroebe)
SVGEE (Bioroebe::SVG)
SanitizeCodonFrequency (Bioroebe)
SanitizeNucleotideSequence (Bioroebe)
ScanForRepeat (Bioroebe)
Score (Bioroebe::ColourScheme)
Sequence (Bioroebe)
Server (Bioroebe::Biomart)
Shared (Bioroebe::Taxonomy)
Shell (Bioroebe)
ShowCodonTable (Bioroebe::GUI::LibUI)
ShowCodonTable (Bioroebe::GUI::Gtk)
ShowCodonTableModule (Bioroebe::GUI)
ShowCodonTables (Bioroebe)
ShowCodonUsage (Bioroebe::GUI::LibUI)
ShowCodonUsage (Bioroebe::GUI::Gtk)
ShowCodonUsage (Bioroebe)
ShowCodonUsageModule (Bioroebe::GUI)
ShowFastaHeaders (Bioroebe)
ShowFastaStatistics (Bioroebe)
ShowHydrophobicity (Bioroebe)
ShowNucleotideSequence (Bioroebe)
ShowOrf (Bioroebe)
ShowRestrictionEnzymes (Bioroebe)
ShowThisCodonTable (Bioroebe)
ShowThisDNASequence (Bioroebe)
SiRNA (Bioroebe)
Simple (Bioroebe::ColourScheme)
SimpleStarFileGenerator (Bioroebe::ElectronMicroscopy)
SimpleStringComparer (Bioroebe)
SimplifyFastaHeader (Bioroebe)
Sinatra (Bioroebe)
Sizeseq (Bioroebe::GUI::Gtk)
SmithWaterman (Bioroebe)
Snapgene (Bioroebe::GUI::Gtk)
SplitThisFastaFileIntoChromosomes (Bioroebe)
Strand (Bioroebe::ColourScheme)
StrideParser (Bioroebe)

T

Taxonomy (Bioroebe)
Taylor (Bioroebe::ColourScheme)
ThreeLetterToAminoacid (Bioroebe::Quiz)
ThreeToOne (Bioroebe::GUI::Gtk)
ThreeToOne (Bioroebe::GUI::Tk)
ThreeToOne (Bioroebe::GUI::LibUI)
ThreeToOneModule (Bioroebe::GUI::Gtk)
Tk (Bioroebe::GUI)
Track (Bioroebe::SVG)
Trypsin (Bioroebe)
Turn (Bioroebe::ColourScheme)

U

UsefulFormulas (Bioroebe)

V

VerboseTruth (Bioroebe)

W

WwwFinder (Bioroebe::GUI::Gtk)

Z

Zappo (Bioroebe::ColourScheme)