CGAT-apps
latest
Mission statement
Installation instructions
Using CGAT Tools
Tool map
Tool reference
Contributing to CGAT code
Reference
Release Notes
Contributing to CGAT code
Testing
Style Guide
Documentation
Reference
Importing CGAT scripts into galaxy
Glossary
CGAT-apps
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
_
__init__
module
A
Accumulate() (in module Histogram)
Add() (in module Histogram)
addAlignments() (in module Blat)
addComplementIntervals() (in module Intervals)
addElement() (SVGdraw.SVGelement method)
addOptions() (in module MatrixTools)
AddOptions() (WrapperCodeML.BaseML method)
(WrapperCodeML.CodeML method)
addProperties() (SequenceProperties.SequenceProperties method)
(SequenceProperties.SequencePropertiesAA method)
(SequenceProperties.SequencePropertiesAminoAcids method)
(SequenceProperties.SequencePropertiesCodons method)
(SequenceProperties.SequencePropertiesCodonTranslator method)
(SequenceProperties.SequencePropertiesCodonUsage method)
(SequenceProperties.SequencePropertiesCounts method)
(SequenceProperties.SequencePropertiesCpg method)
(SequenceProperties.SequencePropertiesDegeneracy method)
(SequenceProperties.SequencePropertiesDN method)
(SequenceProperties.SequencePropertiesEntropy method)
(SequenceProperties.SequencePropertiesGaps method)
(SequenceProperties.SequencePropertiesLength method)
(SequenceProperties.SequencePropertiesNA method)
(SequenceProperties.SequencePropertiesSequence method)
AddRelativeAndCumulativeDistributions() (in module Histogram)
adjustPValues() (in module Stats)
after() (IndexedGenome.Quicksect method)
AGP
module
agp
AGP (class in AGP)
AlignedPair2SubstitutionMatrix() (in module Genomics)
Alignment2CDNA() (in module Genomics)
Alignment2DNA() (in module Genomics)
Alignment2ExonBoundaries() (in module Genomics)
Alignment2PeptideAlignment() (in module Genomics)
Alignment2String() (in module Genomics)
AlignmentProtein2CDNA() (in module Genomics)
animate (class in SVGdraw)
animateColor (class in SVGdraw)
animateMotion (class in SVGdraw)
animateTransform (class in SVGdraw)
asDict() (GTF.Entry method)
asRanges() (in module GTF)
AString
module
AString (class in AString)
attributes (GTF.Entry attribute)
axt
B
bam
bamG
bamT
BamTools
module
BaseML (class in WrapperCodeML)
BaseMLResult (class in WrapperCodeML)
Bed
module
bed
Bed (class in Bed)
bed_iterator() (in module Bed)
before() (IndexedGenome.Quicksect method)
benchmarkRandomFragment() (in module IndexedFasta)
bezier() (SVGdraw.pathdata method)
bigwig
binIntervals() (in module Bed)
bins() (in module cgat.tools.bed2bed)
Blat
module
block() (in module cgat.tools.bed2bed)
blockCount (Bed.Bed attribute)
blocked_iterator() (in module Bed)
blockSizes (Bed.Bed attribute)
blockStarts (Bed.Bed attribute)
Branchlength2Support() (in module TreeTools)
buildAlleles() (in module Variants)
BuildMapSpecies2Genes() (in module TreeTools)
buildMatrixFromEdges() (in module MatrixTools)
buildMatrixFromLists() (in module MatrixTools)
buildMatrixFromTables() (in module MatrixTools)
buildOffsets() (in module Variants)
buildSubstitutionMatrix() (SequencePairProperties.SequencePairPropertiesCountsNa method)
C
Calculate() (in module Histogram)
(in module Histogram2D)
CalculateCAIWeightsFromCounts() (in module Genomics)
CalculateCodonFrequenciesFromCounts() (in module Genomics)
CalculateConst() (in module Histogram)
CalculateFromTable() (in module Histogram)
calculateOverlap() (in module Intervals)
CalculatePairIndices() (in module Genomics)
calculatePatternsFromTree() (in module TreeTools)
CalculateRCSUValuesFromCounts() (in module Genomics)
calculateScale() (WrapperCodeML.Evolver method)
CBioPortal
module
CBioPortal (class in CBioPortal)
CDGSError
cgat.tools.__init__
module
cgat.tools.bam2bam
module
cgat.tools.bam2bed
module
cgat.tools.bam2fastq
module
cgat.tools.bam2geneprofile
module
cgat.tools.bam2peakshape
module
cgat.tools.bam2stats
module
cgat.tools.bam2UniquePairs
module
cgat.tools.bam2wiggle
module
cgat.tools.bam_vs_bam
module
cgat.tools.bam_vs_bed
module
cgat.tools.bams2bam
module
cgat.tools.bcl2fastq
module
cgat.tools.bed2annotator
module
cgat.tools.bed2bed
module
cgat.tools.bed2fasta
module
cgat.tools.bed2gff
module
cgat.tools.bed2graph
module
cgat.tools.bed2plot
module
cgat.tools.bed2stats
module
cgat.tools.beds2beds
module
cgat.tools.beds2counts
module
cgat.tools.cat_tables
module
cgat.tools.cgat2dot
module
cgat.tools.cgat_galaxy_wrapper
module
cgat.tools.cgat_get_options
module
cgat.tools.cgat_pep8_code_quality
module
cgat.tools.cgat_rebuild_extensions
module
cgat.tools.cgat_script_template
module
cgat.tools.chain2psl
module
cgat.tools.combine_tables
module
cgat.tools.csv2csv
module
cgat.tools.csv2db
module
cgat.tools.csv_cut
module
cgat.tools.csv_intersection
module
cgat.tools.csv_rename
module
cgat.tools.csv_select
module
cgat.tools.csv_set
module
cgat.tools.csvs2csv
module
cgat.tools.data2histogram
module
cgat.tools.diff_bam
module
cgat.tools.diff_bed
module
cgat.tools.diff_chains
module
cgat.tools.diff_fasta
module
cgat.tools.diff_gtf
module
cgat.tools.fasta2bed
module
cgat.tools.fasta2fasta
module
cgat.tools.fasta2kmercontent
module
cgat.tools.fasta2variants
module
cgat.tools.fastas2fasta
module
cgat.tools.fastq2fastq
module
cgat.tools.fastq2summary
module
cgat.tools.fastq2table
module
cgat.tools.fastqs2fasta
module
cgat.tools.fastqs2fastq
module
cgat.tools.fastqs2fastqs
module
cgat.tools.genome_bed
module
cgat.tools.gff2bed
module
cgat.tools.gff2coverage
module
cgat.tools.gff2fasta
module
cgat.tools.gff2gff
module
cgat.tools.gff2histogram
module
cgat.tools.gff2psl
module
cgat.tools.gff2stats
module
cgat.tools.gff2table
module
cgat.tools.gff32gtf
module
cgat.tools.gtf2fasta
module
cgat.tools.gtf2gff
module
cgat.tools.gtf2gtf
module
cgat.tools.gtf2tsv
module
cgat.tools.gtfs2tsv
module
cgat.tools.index2bed
module
cgat.tools.index_fasta
module
cgat.tools.medip_merge_intervals
module
cgat.tools.metaphlan2table
module
cgat.tools.rnaseq_junction_bam2bam
module
cgat.tools.split_fasta
module
cgat.tools.split_file
module
cgat.tools.split_gff
module
cgat.tools.table2table
module
cgat.tools.transfac2transfac
module
cgat.tools.vcf2vcf
module
cgat.tools.vcfstats2db
module
cgat.tools.wig2bed
module
cgatIndexedFasta (class in IndexedFasta)
checkSection() (WrapperCodeML.CodeML method)
chrom_iterator() (in module GFF3)
chunk_iterator() (in module GTF)
circle (class in SVGdraw)
clean_cache() (in module Sra)
closepath() (SVGdraw.pathdata method)
code directory
CodeML (class in WrapperCodeML)
CodeMLAncestralSequence (class in WrapperCodeML)
CodeMLBranchInfo (class in WrapperCodeML)
CodeMLPairwise (class in WrapperCodeML)
CodeMLResultPair (class in WrapperCodeML)
CodeMLResultPairs (class in WrapperCodeML)
CodeMLResultSites (class in WrapperCodeML)
CodeMLSites (class in WrapperCodeML)
columns() (Bed.Bed property)
combinations() (in module SetTools)
Combine() (in module Histogram)
combine() (in module Intervals)
combineAtDistance() (in module Intervals)
CombineOverlaps() (in module GTF)
compareLists() (in module SetTools)
complement() (in module Intervals)
compress() (in module RLE)
compressIndex() (IndexedFasta.cgatIndexedFasta method)
computeROC() (in module Stats)
contig (Bed.Bed attribute)
(GTF.Entry attribute)
convert() (in module Histogram)
convertCoordinates() (Blat.Match method)
convertStrand() (in module Genomics)
convertTree2Graph() (in module TreeTools)
copy() (Bed.Bed method)
(GTF.Entry method)
CorrelationTest (class in Stats)
count() (in module FastaIterator)
Count() (in module Histogram)
CountBranchPoints() (in module TreeTools)
CountCodons() (in module Genomics)
CountDuplications() (in module TreeTools)
CountGeneFeatures() (in module Genomics)
countMotifs() (in module Motifs)
countSubstitutions() (in module RateEstimation)
createDatabase() (in module IndexedFasta)
Cumulate() (in module Histogram)
cumulate() (in module Histogram)
cursor (class in SVGdraw)
D
decode() (in module RLE)
decodeGenotype() (in module Genomics)
defs (class in SVGdraw)
description (class in SVGdraw)
dfs() (Tree.Tree method)
dictzip
module
DistributionalParameters (class in Stats)
doBinomialTest() (in module Stats)
doChiSquaredTest() (in module Stats)
doCorrelationTest() (in module Stats)
Documentation() (in module cgat.tools.vcf2vcf)
doFDRPython() (in module Stats)
doLogLikelihoodTest() (in module Stats)
doMannWhitneyUTest() (in module Stats)
doPairedTTest() (in module Stats)
doPearsonChiSquaredTest() (in module Stats)
doWelchsTTest() (in module Stats)
drawing (class in SVGdraw)
E
edge list
,
[1]
ellarc() (SVGdraw.pathdata method)
ellipse (class in SVGdraw)
encode() (in module RLE)
encodeGenotype() (in module Genomics)
end (Bed.Bed attribute)
(GTF.Entry attribute)
Entry (class in GFF3)
(class in GTF)
environment variable
PYTHONPATH
Error
,
[1]
,
[2]
evaluateCodonPair() (in module RateEstimation)
Evolver (class in WrapperCodeML)
EvolverBaseml (class in WrapperCodeML)
execution host
Exons2Alignment() (in module Genomics)
experiment
ExtendedVariant (in module Variants)
extract() (in module Sra)
F
fasta
FastaIterator
module
FastaIterator (class in FastaIterator)
FastaRecord (class in FastaIterator)
Fastq
module
fastq
,
[1]
feature (GTF.Entry attribute)
fetch_ENA() (in module Sra)
fetch_ENA_files() (in module Sra)
fetch_TCGA_BAM() (in module Sra)
fetch_TCGA_fastq() (in module Sra)
fileno() (dictzip.GzipFile method)
Fill() (in module Histogram)
fill() (in module Histogram)
fillHistograms() (in module Histogram)
filterMasked() (in module Stats)
flat_file_iterator() (in module GFF3)
flat_gene_iterator() (in module GTF)
fn() (Stats.ROCResult property)
fnr() (Stats.ROCResult property)
fold (FastaIterator.FastaRecord attribute)
forceForwardCoordinates() (in module Genomics)
format (Fastq.Record attribute)
fp() (Stats.ROCResult property)
fpr() (Stats.ROCResult property)
frame (GTF.Entry attribute)
fromArray() (in module Intervals)
fromBed() (GTF.Entry method)
fromGTF() (Bed.Bed method)
(GTF.Entry method)
fromIntervals() (Bed.Bed method)
fromMali() (WrapperCodeML.Evolver method)
(WrapperCodeML.EvolverBaseml method)
fromMap() (Blat.Match method)
fromMaq() (Blat.Match method)
fromPair() (Blat.Match method)
fromPhred() (Fastq.Record method)
fromPSL() (Blat.MatchPSLX method)
fromResult() (WrapperCodeML.CodeMLResultPairs method)
G
gdl
gene_id (GTF.Entry attribute)
gene_iterator() (in module GTF)
Genes2Species() (in module TreeTools)
Genomics
module
genotype() (Variants.Variant property)
get() (IndexedGenome.IndexedGenome method)
(IndexedGenome.Quicksect method)
get_leaves() (Tree.Tree method)
get_nodes() (Tree.Tree method)
GetAlignmentLength() (in module Genomics)
getAllCombinations() (in module SetTools)
GetAllNodes() (in module TreeTools)
getAlphabet() (Masker.Masker method)
getAreaUnderCurve() (in module Stats)
getAttributeField() (GFF3.Entry method)
GetBiasedCodonUsage() (in module Genomics)
getBlocks() (Blat.Match method)
GetBranchLengths() (in module TreeTools)
getCancerStudies() (CBioPortal.CBioPortal method)
getCaseLists() (CBioPortal.CBioPortal method)
GetChildNodesWhereTrue() (in module TreeTools)
getClinicalData() (CBioPortal.CBioPortal method)
GetCommonAncestor() (in module TreeTools)
getComponents() (in module Blat)
getContigs() (IndexedFasta.cgatIndexedFasta method)
getContigSizes() (IndexedFasta.cgatIndexedFasta method)
getConverter() (in module IndexedFasta)
getCounts() (in module Motifs)
getDatabaseName() (IndexedFasta.cgatIndexedFasta method)
GetDegenerateSites() (in module Genomics)
getDistanceGTR() (in module RateEstimation)
GetDistancesBetweenTaxa() (in module TreeTools)
GetDistanceToRoot() (in module TreeTools)
getEntropy() (SequenceProperties.SequencePropertiesBias method)
(SequenceProperties.SequencePropertiesEntropy method)
getGCContent() (Genomics.SequencePairInfo method)
getGeneticProfiles() (CBioPortal.CBioPortal method)
getHeader() (Stats.DistributionalParameters method)
(Stats.Summary method)
getHeaders() (SequenceProperties.SequencePropertiesAA method)
(Stats.DistributionalParameters method)
(Stats.Summary method)
GetHID() (in module Genomics)
getIntersections() (in module Intervals)
GetIntronType() (in module Genomics)
getKL() (SequenceProperties.SequencePropertiesBias method)
GetLeaves() (in module TreeTools)
getLength() (in module Intervals)
(IndexedFasta.cgatIndexedFasta method)
getLengths() (IndexedFasta.cgatIndexedFasta method)
getLink() (CBioPortal.CBioPortal method)
GetMapAA2Codons() (in module Genomics)
getMapQuery2Target() (Blat.Match method)
getMapTarget2Query() (Blat.Match method)
getMatrixFromEdges() (in module MatrixTools)
GetMaxIndex() (in module TreeTools)
getMessageLength() (SequenceProperties.SequencePropertiesBias method)
GetMonophyleticPairs() (in module TreeTools)
getMutationData() (CBioPortal.CBioPortal method)
GetNodeMap() (in module TreeTools)
getNumColumns() (in module Bed)
getNumLeaves() (Tree.Tree method)
getOccurances() (in module Motifs)
getOffset() (in module Fastq)
getOncoprintHTML() (CBioPortal.CBioPortal method)
getOptions() (in module WrapperCodeML)
GetOptions() (WrapperCodeML.CodeML method)
getParameters() (WrapperCodeML.EvolverBaseml method)
GetParentNodeWhereTrue() (in module TreeTools)
getPercentAltered() (CBioPortal.CBioPortal method)
getPerformance() (in module Stats)
getPooledVariance() (in module Stats)
getProfileData() (CBioPortal.CBioPortal method)
getProteinArrayData() (CBioPortal.CBioPortal method)
getProteinArrayInfo() (CBioPortal.CBioPortal method)
getQMatrix() (in module RateEstimation)
getRandomCoordinates() (IndexedFasta.cgatIndexedFasta method)
getRateMatrix() (in module RateEstimation)
getReadLength() (in module Fastq)
getSection() (WrapperCodeML.CodeML method)
getSensitivityRecall() (in module Stats)
getSequence() (IndexedFasta.cgatIndexedFasta method)
(IndexedFasta.PysamIndexedFasta method)
getSignificance() (in module Stats)
GetSize() (in module TreeTools)
GetSubsets() (in module TreeTools)
GetSubtree() (in module TreeTools)
GetTaxa() (in module TreeTools)
GetTaxaForSpecies() (in module TreeTools)
GetTaxonomicNames() (in module TreeTools)
getToken() (IndexedFasta.cgatIndexedFasta method)
getTotalAltered() (CBioPortal.CBioPortal method)
GetUniformCodonUsage() (in module Genomics)
getZScore() (Stats.DistributionalParameters method)
gff
GFF3
module
Glam2
module
Glam2Scan
module
go
goslim
graph
,
[1]
Graph2Tree() (in module TreeTools)
group (class in SVGdraw)
group_by_distance() (in module Iterators)
grouped_iterator() (in module Bed)
GTF
module
gtf
guessDataType() (Fastq.Record method)
(in module Fastq)
guessFormat() (Fastq.Record method)
(in module Fastq)
GzipFile (class in dictzip)
H
HalfIdentity() (in module GTF)
hasOverlap() (GTF.Entry method)
Histogram
module
histogram() (in module Histogram)
Histogram2D
module
hline() (SVGdraw.pathdata method)
I
identifier (Fastq.Record attribute)
Identity() (in module GTF)
IGV
module
IGV (class in IGV)
image (class in SVGdraw)
index_factory (IndexedGenome.IndexedGenome attribute)
(IndexedGenome.Simple attribute)
IndexedFasta
module
IndexedFasta() (in module IndexedFasta)
IndexedGenome
module
IndexedGenome (class in IndexedGenome)
indexVariants() (in module Variants)
initializeQMatrix() (in module RateEstimation)
intersect() (in module Intervals)
Intervals
module
invert() (GTF.Entry method)
IsCompatible() (in module TreeTools)
isHalfIdentical() (GTF.Entry method)
isIdentical() (GTF.Entry method)
IsJunk() (in module Genomics)
IsMonophyleticForSpecies() (in module TreeTools)
IsMonophyleticForTaxa() (in module TreeTools)
IsSingleSpecies() (in module TreeTools)
itemRGB (Bed.Bed attribute)
iterate() (in module FastaIterator)
(in module Fastq)
iterate_convert() (in module Fastq)
iterate_guess() (in module Fastq)
iterate_together() (in module FastaIterator)
iterator() (in module Bed)
(in module Blat)
(in module GTF)
iterator2() (in module Blat)
iterator_contigs() (in module GTF)
iterator_filtered() (in module GTF)
iterator_from_gff() (in module GFF3)
iterator_min_feature_length() (in module GTF)
iterator_overlapping_genes() (in module GTF)
iterator_overlaps() (in module GTF)
iterator_per_query() (in module Blat)
iterator_pslx() (in module Blat)
iterator_query_overlap() (in module Blat)
iterator_sorted() (in module GTF)
iterator_sorted_chunks() (in module GTF)
iterator_target_overlap() (in module Blat)
iterator_test() (in module Blat)
iterator_transcripts2genes() (in module GTF)
Iterators
module
iupac2regex() (in module Motifs)
J
joined_iterator() (in module GTF)
(in module Intervals)
L
line (class in SVGdraw)
line() (SVGdraw.pathdata method)
lineargradient (class in SVGdraw)
link (class in SVGdraw)
loadPair() (SequencePairProperties.SequencePairPropertiesBaseML method)
(SequencePairProperties.SequencePairPropertiesCountsNa method)
(SequencePairProperties.SequencePairPropertiesPID method)
loadSequence() (SequenceProperties.SequenceProperties method)
(SequenceProperties.SequencePropertiesAA method)
(SequenceProperties.SequencePropertiesAminoAcids method)
(SequenceProperties.SequencePropertiesCodons method)
(SequenceProperties.SequencePropertiesCodonTranslator method)
(SequenceProperties.SequencePropertiesCounts method)
(SequenceProperties.SequencePropertiesCpg method)
(SequenceProperties.SequencePropertiesDegeneracy method)
(SequenceProperties.SequencePropertiesDN method)
(SequenceProperties.SequencePropertiesGaps method)
(SequenceProperties.SequencePropertiesHid method)
(SequenceProperties.SequencePropertiesLength method)
(SequenceProperties.SequencePropertiesNA method)
(SequenceProperties.SequencePropertiesSequence method)
loglevel
lower() (AString.AString method)
M
makeSubstitutionMatrix() (in module Genomics)
MapCodon2AA() (in module Genomics)
mapLocation() (AGP.AGP method)
MapTaxa() (in module TreeTools)
MapTerminalTaxa() (in module TreeTools)
marker (class in SVGdraw)
Masker
module
Masker (class in Masker)
MaskerBias (class in Masker)
MaskerDustMasker (class in Masker)
MaskerRandom (class in Masker)
MaskerSeg (class in Masker)
maskSequence() (Masker.Masker method)
maskSequences() (in module Masker)
(Masker.Masker method)
MaskStopCodons() (in module Genomics)
Match (class in Blat)
(class in Glam2Scan)
MatchPSLX (class in Blat)
MatrixTools
module
merge() (in module Bed)
(in module cgat.tools.bed2bed)
merged_gene_iterator() (in module GTF)
mergeVariants() (in module Variants)
module
__init__
AGP
AString
BamTools
Bed
Blat
CBioPortal
cgat.tools.__init__
cgat.tools.bam2bam
cgat.tools.bam2bed
cgat.tools.bam2fastq
cgat.tools.bam2geneprofile
cgat.tools.bam2peakshape
cgat.tools.bam2stats
cgat.tools.bam2UniquePairs
cgat.tools.bam2wiggle
cgat.tools.bam_vs_bam
cgat.tools.bam_vs_bed
cgat.tools.bams2bam
cgat.tools.bcl2fastq
cgat.tools.bed2annotator
cgat.tools.bed2bed
cgat.tools.bed2fasta
cgat.tools.bed2gff
cgat.tools.bed2graph
cgat.tools.bed2plot
cgat.tools.bed2stats
cgat.tools.beds2beds
cgat.tools.beds2counts
cgat.tools.cat_tables
cgat.tools.cgat2dot
cgat.tools.cgat_galaxy_wrapper
cgat.tools.cgat_get_options
cgat.tools.cgat_pep8_code_quality
cgat.tools.cgat_rebuild_extensions
cgat.tools.cgat_script_template
cgat.tools.chain2psl
cgat.tools.combine_tables
cgat.tools.csv2csv
cgat.tools.csv2db
cgat.tools.csv_cut
cgat.tools.csv_intersection
cgat.tools.csv_rename
cgat.tools.csv_select
cgat.tools.csv_set
cgat.tools.csvs2csv
cgat.tools.data2histogram
cgat.tools.diff_bam
cgat.tools.diff_bed
cgat.tools.diff_chains
cgat.tools.diff_fasta
cgat.tools.diff_gtf
cgat.tools.fasta2bed
cgat.tools.fasta2fasta
cgat.tools.fasta2kmercontent
cgat.tools.fasta2variants
cgat.tools.fastas2fasta
cgat.tools.fastq2fastq
cgat.tools.fastq2summary
cgat.tools.fastq2table
cgat.tools.fastqs2fasta
cgat.tools.fastqs2fastq
cgat.tools.fastqs2fastqs
cgat.tools.genome_bed
cgat.tools.gff2bed
cgat.tools.gff2coverage
cgat.tools.gff2fasta
cgat.tools.gff2gff
cgat.tools.gff2histogram
cgat.tools.gff2psl
cgat.tools.gff2stats
cgat.tools.gff2table
cgat.tools.gff32gtf
cgat.tools.gtf2fasta
cgat.tools.gtf2gff
cgat.tools.gtf2gtf
cgat.tools.gtf2tsv
cgat.tools.gtfs2tsv
cgat.tools.index2bed
cgat.tools.index_fasta
cgat.tools.medip_merge_intervals
cgat.tools.metaphlan2table
cgat.tools.rnaseq_junction_bam2bam
cgat.tools.split_fasta
cgat.tools.split_file
cgat.tools.split_gff
cgat.tools.table2table
cgat.tools.transfac2transfac
cgat.tools.vcf2vcf
cgat.tools.vcfstats2db
cgat.tools.wig2bed
dictzip
FastaIterator
Fastq
Genomics
GFF3
Glam2
Glam2Scan
GTF
Histogram
Histogram2D
IGV
IndexedFasta
IndexedGenome
Intervals
Iterators
Masker
MatrixTools
Motifs
RateEstimation
RLE
SequencePairProperties
SequenceProperties
SetTools
Sra
Stats
SVGdraw
tools.bam_vs_gtf
Tree
TreeTools
Variants
VCF
WrapperCodeML
Motifs
module
move() (SVGdraw.pathdata method)
N
name (Bed.Bed attribute)
Newick2Nexus() (in module TreeTools)
Newick2Tree() (in module TreeTools)
Nexus2Newick() (in module TreeTools)
Nop() (in module Tree)
normalize() (in module Histogram)
O
open() (in module dictzip)
Overlap() (in module GTF)
P
PairedTTest (class in Stats)
parse() (in module Glam2)
(in module Glam2Scan)
parse_region_string() (in module Genomics)
parseCoordinates() (in module IndexedFasta)
ParseFasta2Hash() (in module Genomics)
parseFrequencies() (WrapperCodeML.BaseML method)
parseGrids() (WrapperCodeML.CodeMLSites method)
parseInfo() (GFF3.Entry method)
(GTF.Entry method)
parseLog() (WrapperCodeML.CodeML method)
(WrapperCodeML.CodeMLPairwise method)
parseOutput() (WrapperCodeML.BaseML method)
(WrapperCodeML.CodeML method)
(WrapperCodeML.CodeMLPairwise method)
(WrapperCodeML.CodeMLSites method)
parsePairs() (WrapperCodeML.CodeMLPairwise method)
parseRst() (WrapperCodeML.CodeML method)
parseSites() (WrapperCodeML.CodeMLSites method)
ParsingError
,
[1]
,
[2]
path (class in SVGdraw)
pathdata (class in SVGdraw)
pattern (class in SVGdraw)
peek() (in module Sra)
point (class in SVGdraw)
polygon (class in SVGdraw)
polyline (class in SVGdraw)
pos() (Variants.Variant property)
pred() (Stats.ROCResult property)
prefetch() (in module Sra)
Print() (in module Histogram)
(in module Histogram2D)
PrintAscii() (in module Histogram)
printPrettyAlignment() (in module Genomics)
process_remote_BAM() (in module Sra)
production pipeline
project pipeline
prune() (in module Intervals)
PruneTerminal() (in module TreeTools)
PruneTree() (in module TreeTools)
psl
pvalue() (Stats.PairedTTest property)
PysamIndexedFasta (class in IndexedFasta)
PYTHONPATH
Q
qbezier() (SVGdraw.pathdata method)
quals (Fastq.Record attribute)
query
Quicksect (class in IndexedGenome)
quote() (in module GTF)
R
radialgradient (class in SVGdraw)
RateEstimation
module
rdf
read() (GTF.Entry method)
readAndIndex() (in module Bed)
(in module GTF)
readAsIntervals() (in module GTF)
readContigSizes() (in module Genomics)
readFromFile() (AGP.AGP method)
(in module GTF)
ReadPeptideSequences() (in module Genomics)
ReconciliateByRio() (in module TreeTools)
Record (class in Fastq)
rect (class in SVGdraw)
reference() (Variants.Variant property)
regex2iupac() (in module Motifs)
relabel() (Tree.Tree method)
relbezier() (SVGdraw.pathdata method)
relellarc() (SVGdraw.pathdata method)
relhline() (SVGdraw.pathdata method)
relline() (SVGdraw.pathdata method)
relmove() (SVGdraw.pathdata method)
relqbezier() (SVGdraw.pathdata method)
relsmbezier() (SVGdraw.pathdata method)
relsmqbezier() (SVGdraw.pathdata method)
relvline() (SVGdraw.pathdata method)
RemoveFrameShiftsFromAlignment() (in module Genomics)
RemoveIntervalsContained() (in module Intervals)
RemoveIntervalsSpanning() (in module Intervals)
replicate
Reroot() (in module TreeTools)
rescaleBranchLengths() (Tree.Tree method)
resolveAmbiguousNA() (in module Genomics)
resolveReverseAmbiguousNA() (in module Genomics)
Result (class in Stats)
reverse_complement() (in module Genomics)
rewind() (dictzip.GzipFile method)
rfnr() (Stats.ROCResult property)
RLE
module
ROCResult (class in Stats)
root_at_node() (Tree.Tree method)
root_balanced() (Tree.Tree method)
root_midpoint() (Tree.Tree method)
rtpr() (Stats.ROCResult property)
run() (WrapperCodeML.Evolver method)
runEvolver() (in module WrapperCodeML)
S
sam
sample() (in module Iterators)
savitzky_golay() (in module Stats)
Scale() (in module Histogram)
score (Bed.Bed attribute)
(GTF.Entry attribute)
script (class in SVGdraw)
seq (Fastq.Record attribute)
sequence (FastaIterator.FastaRecord attribute)
SequencePairInfo (class in Genomics)
SequencePairInfoCodons (class in Genomics)
SequencePairProperties
module
SequencePairPropertiesBaseML (class in SequencePairProperties)
SequencePairPropertiesCountsCodons (class in SequencePairProperties)
SequencePairPropertiesCountsNa (class in SequencePairProperties)
SequencePairPropertiesDistance (class in SequencePairProperties)
SequencePairPropertiesPID (class in SequencePairProperties)
SequenceProperties
module
SequenceProperties (class in SequenceProperties)
SequencePropertiesAA (class in SequenceProperties)
SequencePropertiesAminoAcids (class in SequenceProperties)
SequencePropertiesBias (class in SequenceProperties)
SequencePropertiesCodons (class in SequenceProperties)
SequencePropertiesCodonTranslator (class in SequenceProperties)
SequencePropertiesCodonUsage (class in SequenceProperties)
SequencePropertiesCounts (class in SequenceProperties)
SequencePropertiesCpg (class in SequenceProperties)
SequencePropertiesDegeneracy (class in SequenceProperties)
SequencePropertiesDN (class in SequenceProperties)
SequencePropertiesEntropy (class in SequenceProperties)
SequencePropertiesGaps (class in SequenceProperties)
SequencePropertiesHid (class in SequenceProperties)
SequencePropertiesLength (class in SequenceProperties)
SequencePropertiesNA (class in SequenceProperties)
SequencePropertiesSequence (class in SequenceProperties)
set (class in SVGdraw)
setConverter() (IndexedFasta.cgatIndexedFasta method)
setDefaultCaseList() (CBioPortal.CBioPortal method)
setDefaultStudy() (CBioPortal.CBioPortal method)
setFormat() (Stats.DistributionalParameters method)
setFrequencies() (in module RateEstimation)
setName() (in module Bed)
SetOptions() (WrapperCodeML.BaseML method)
(WrapperCodeML.CodeML method)
SetTools
module
setTranslator() (IndexedFasta.cgatIndexedFasta method)
setTree() (WrapperCodeML.Evolver method)
setUniformFrequencies() (WrapperCodeML.Evolver method)
(WrapperCodeML.EvolverBaseml method)
shift() (in module cgat.tools.bed2bed)
ShortenIntervalsOverlap() (in module Intervals)
Simple (class in IndexedGenome)
smbezier() (SVGdraw.pathdata method)
SmoothWrap() (in module Histogram)
smqbezier() (SVGdraw.pathdata method)
sort() (IGV.IGV method)
SortPerContig() (in module GTF)
source (GTF.Entry attribute)
spannedtext (class in SVGdraw)
Species2Genes() (in module TreeTools)
sphinxreport
splitFasta() (in module IndexedFasta)
Sra
module
sra
start (Bed.Bed attribute)
(GTF.Entry attribute)
startIGV() (in module IGV)
statistic() (Stats.PairedTTest property)
Stats
module
stderr
stdin
stdout
stop (class in SVGdraw)
strand (Bed.Bed attribute)
(GTF.Entry attribute)
String2Alignment() (in module Genomics)
String2Location() (in module Genomics)
style (class in SVGdraw)
submit host
Summary (class in Stats)
svg
(class in SVGdraw)
SVGdraw
module
SVGelement (class in SVGdraw)
switch (class in SVGdraw)
switchTargetStrand() (Blat.Match method)
symbol (class in SVGdraw)
T
target
task
test directory
text (class in SVGdraw)
textpath (class in SVGdraw)
thickEnd (Bed.Bed attribute)
thickStart (Bed.Bed attribute)
title (class in SVGdraw)
(FastaIterator.FastaRecord attribute)
tn() (Stats.ROCResult property)
tnr() (Stats.ROCResult property)
to_string() (Tree.Tree method)
toDot() (in module GTF)
toIntervals() (Bed.Bed method)
toIntronIntervals() (in module GTF)
tools.bam_vs_gtf
module
toPhred() (Fastq.Record method)
toSequence() (in module GTF)
tp() (Stats.ROCResult property)
tpr() (Stats.ROCResult property)
track
Track (class in Bed)
track_iterator() (in module GTF)
Transcript2GeneTree() (in module TreeTools)
transcript_id (GTF.Entry attribute)
transcript_iterator() (in module GTF)
translate() (in module Genomics)
TranslateDNA2Protein() (in module Genomics)
Translator (class in IndexedFasta)
TranslatorBytes (class in IndexedFasta)
TranslatorPhred (class in IndexedFasta)
TranslatorRange200 (class in IndexedFasta)
TranslatorSolexa (class in IndexedFasta)
traverseGraph() (in module TreeTools)
Tree
module
Tree (class in Tree)
Tree2Graph() (in module TreeTools)
Tree2Newick() (in module TreeTools)
TreeDFS() (in module TreeTools)
TreeTools
module
tref (class in SVGdraw)
trim() (Fastq.Record method)
trim5() (Fastq.Record method)
truncate() (in module Intervals)
(Tree.Tree method)
tspan (class in SVGdraw)
tss
tsv
U
unionIntersectionMatrix() (in module SetTools)
Unroot() (in module TreeTools)
updateNexus() (in module Tree)
updateProperties() (SequenceProperties.SequencePropertiesDegeneracy method)
(Stats.DistributionalParameters method)
updateVariants() (in module Variants)
upper() (AString.AString method)
UsageError
use (class in SVGdraw)
V
value() (Stats.ROCResult property)
Variant (class in Variants)
Variants
module
VCF
module
vcf
VCFEntry (class in VCF)
VCFFile (class in VCF)
verify() (in module IndexedFasta)
view (class in SVGdraw)
vline() (SVGdraw.pathdata method)
W
wiggle
WrapperCodeML
module
Write() (in module Histogram)
WriteAlignment() (WrapperCodeML.CodeML method)
writeControlFile() (WrapperCodeML.CodeML method)
(WrapperCodeML.Evolver method)
(WrapperCodeML.EvolverBaseml method)
writeFragments() (in module IndexedFasta)
WriteNexus() (in module TreeTools)
writeSets() (in module SetTools)
writeToFile() (Tree.Tree method)
WriteTree() (WrapperCodeML.CodeML method)
X
xuniqueCombinations() (in module SetTools)
Y
yaml
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds