Documentation for BioDSL (1.0.2)

Alphabetic Index

File Listing

README

Namespace Listing A-Z

A

AddKey (BioDSL)
AlignSeqMothur (BioDSL)
Ambiguity (BioDSL)
AnalyzeResidueDistribution (BioDSL)
Array
Assemble (BioDSL)
AssemblePairs (BioDSL)
AssembleSeqIdba (BioDSL)
AssembleSeqRay (BioDSL)
AssembleSeqSpades (BioDSL)
AuxHelper (BioDSL)

B

BackTrack (BioDSL)
BackTrackError (BioDSL)
BioDSL

C

CAry (BioDSL)
CAryError (BioDSL)
CSV (BioDSL)
CSVError (BioDSL)
Channel (BioDSL)
ClassifySeq (BioDSL)
ClassifySeqMothur (BioDSL)
ClipPrimer (BioDSL)
ClusterOtus (BioDSL)
CollapseOtus (BioDSL)
CollectOtus (BioDSL)
Command (BioDSL)
Commands (BioDSL)
ComplementSeq (BioDSL)
Config (BioDSL)
Count (BioDSL)
CountValues (BioDSL)

D

DegapSeq (BioDSL)
DereplicateSeq (BioDSL)
Digest (BioDSL)
Dump (BioDSL)
Dynamic (BioDSL)
DynamicError (BioDSL)

E

EmailHelper (BioDSL)

F

Fasta (BioDSL)
FastaError (BioDSL)
Fastq (BioDSL)
FastqError (BioDSL)
Filesys (BioDSL)
FilesysError (BioDSL)
FilterRrna (BioDSL)
Fork (BioDSL)

G

Genecall (BioDSL)
Grab (BioDSL)

H

Hamming (BioDSL)
HistoryHelper (BioDSL)
Homopolymer (BioDSL)
Homopolymer (BioDSL::Homopolymer)
HomopolymerError (BioDSL)
HtmlReport (BioDSL)

I

IO (BioDSL::Usearch)
IO (BioDSL::Fastq)
IO (BioDSL::Fasta)
IO (BioDSL::CSV)
Index (BioDSL::Taxonomy)
IndexTaxonomy (BioDSL)

K

Kmer (BioDSL)
KmerError (BioDSL)

L

Levenshtein (BioDSL)
LogHelper (BioDSL)

M

MaskSeq (BioDSL)
Match (BioDSL::BackTrack)
Match (BioDSL::Dynamic)
Match (BioDSL::Mummer)
Math (BioDSL)
MeanScores (BioDSL)
MergePairSeq (BioDSL)
MergeTable (BioDSL)
MergeValues (BioDSL)
Mummer (BioDSL)

N

N50 (BioDSL::AssembleSeqRay)
Node (BioDSL::Taxonomy::Search)
Numeric

O

OptionsHelper (BioDSL)
Orf (BioDSL::Seq)

P

Pipeline (BioDSL)
PlotHeatmap (BioDSL)
PlotHistogram (BioDSL)
PlotMatches (BioDSL)
PlotResidueDistribution (BioDSL)
PlotScores (BioDSL)
PosIndex (BioDSL::SliceAlign)

R

Random (BioDSL)
ReadFasta (BioDSL)
ReadFastq (BioDSL)
ReadTable (BioDSL)
Result (BioDSL::Taxonomy::Search)
ReverseSeq (BioDSL)

S

Search (BioDSL::Taxonomy)
Seq (BioDSL)
SeqError (BioDSL)
Serializer (BioDSL)
SliceAlign (BioDSL)
SliceSeq (BioDSL)
Sort (BioDSL)
SplitPairSeq (BioDSL)
SplitValues (BioDSL)
StatusHelper (BioDSL)
Stream (BioDSL)
String

T

TaxNode (BioDSL::Taxonomy::Index)
TaxPath (BioDSL::Taxonomy::Search)
Taxonomy (BioDSL)
TaxonomyError (BioDSL)
TmpDir (BioDSL)
Translate (BioDSL)
Trim (BioDSL)
TrimError (BioDSL)
TrimPrimer (BioDSL)
TrimSeq (BioDSL)

U

UchimeRef (BioDSL)
Uclust (BioDSL)
UniqueValues (BioDSL)
Usearch (BioDSL)
UsearchError (BioDSL)
UsearchGlobal (BioDSL)
UsearchLocal (BioDSL)

W

WriteFasta (BioDSL)
WriteFastq (BioDSL)
WriteTable (BioDSL)
WriteTree (BioDSL)